diff --git a/src/renderer/src/components/sidebar/SetupScriptPromptCard.test.ts b/src/renderer/src/components/sidebar/SetupScriptPromptCard.test.ts
index 192967a14e9..f01e7909a2e 100644
--- a/src/renderer/src/components/sidebar/SetupScriptPromptCard.test.ts
+++ b/src/renderer/src/components/sidebar/SetupScriptPromptCard.test.ts
@@ -1,5 +1,8 @@
 import { describe, expect, it } from 'vitest'
-import { getRenderedSetupScriptPromptState } from './setup-script-prompt-render-state'
+import {
+  getRenderedSetupScriptPromptState,
+  markSetupScriptPromptSaved
+} from './setup-script-prompt-render-state'
 import type { SetupScriptPromptInspection } from '@/lib/setup-script-prompt'
 import { getRepoHostIdentityForParts } from '@/store/slices/repo-host-identity'
 
@@ -87,3 +90,20 @@ describe('getRenderedSetupScriptPromptState', () => {
     ).toBeNull()
   })
 })
+
+describe('markSetupScriptPromptSaved', () => {
+  it('does not apply a completed save to the same repo id on another host', () => {
+    const remote = prompt('repo-orca', 'runtime:windows')
+
+    expect(markSetupScriptPromptSaved(remote, repoIdentity('repo-orca', 'local'))).toBe(remote)
+  })
+
+  it('marks the prompt for the saved host effective', () => {
+    expect(
+      markSetupScriptPromptSaved(
+        prompt('repo-orca', 'runtime:windows'),
+        repoIdentity('repo-orca', 'runtime:windows')
+      )
+    ).toMatchObject({ hasEffectiveSetup: true })
+  })
+})
diff --git a/src/renderer/src/components/sidebar/SetupScriptPromptCard.tsx b/src/renderer/src/components/sidebar/SetupScriptPromptCard.tsx
index 0f64bb6989b..45cb2842e11 100644
--- a/src/renderer/src/components/sidebar/SetupScriptPromptCard.tsx
+++ b/src/renderer/src/components/sidebar/SetupScriptPromptCard.tsx
@@ -21,12 +21,14 @@ import { openSetupScriptSettings } from './open-setup-script-settings'
 import { trackSetupScriptPromptExposure } from './setup-script-prompt-exposure-telemetry'
 import {
   getRenderedSetupScriptPromptState,
+  markSetupScriptPromptSaved,
   type LastVisibleSetupScriptPrompt,
   type SetupScriptPromptState
 } from './setup-script-prompt-render-state'
 import { useSetupScriptPromptRevalidation } from './useSetupScriptPromptRevalidation'
 import { translate } from '@/i18n/i18n'
 import { findRepoForHost, getRepoHostIdentity } from '@/store/slices/repo-host-identity'
+import { getRepoExecutionHostId } from '../../../../shared/execution-host'
 
 function SetupScriptPromptCard(): React.JSX.Element | null {
   const sidebarOpen = useAppStore((s) => s.sidebarOpen)
@@ -41,7 +43,7 @@ function SetupScriptPromptCard(): React.JSX.Element | null {
   const dismissSetupScriptPrompt = useAppStore((s) => s.dismissSetupScriptPrompt)
   const [promptState, setPromptState] = useState<SetupScriptPromptState | null>(null)
   const [detectedSetupDraft, setDetectedSetupDraft] = useState('')
-  const [isImporting, setIsImporting] = useState(false)
+  const [importingRepoHostIdentity, setImportingRepoHostIdentity] = useState<string | null>(null)
   const [inspectionRetryKey, setInspectionRetryKey] = useState(0)
   const trackedPromptKeysRef = useRef<Set<string>>(new Set())
   const mountedRef = useMountedRef()
@@ -50,8 +52,9 @@ function SetupScriptPromptCard(): React.JSX.Element | null {
     () => (activeRepoId ? findRepoForHost(repos, activeRepoId, { settings }) : null),
     [activeRepoId, repos, settings]
   )
-  const isDismissed = activeRepo
-    ? isSetupScriptPromptDismissed(activeRepo.id, dismissedRepoIds)
+  const activeRepoHostIdentity = activeRepo ? getRepoHostIdentity(activeRepo) : null
+  const isDismissed = activeRepoHostIdentity
+    ? isSetupScriptPromptDismissed(activeRepoHostIdentity, dismissedRepoIds)
     : false
   const lastVisiblePromptRef = useRef<LastVisibleSetupScriptPrompt | null>(null)
 
@@ -124,6 +127,7 @@ function SetupScriptPromptCard(): React.JSX.Element | null {
       !isGitRepoKind(activeRepo) ||
       isDismissed ||
       promptState?.repoId !== activeRepo.id ||
+      promptState.repoHostIdentity !== activeRepoHostIdentity ||
       promptState.status !== 'ok' ||
       promptState.hasEffectiveSetup
     ) {
@@ -132,10 +136,11 @@ function SetupScriptPromptCard(): React.JSX.Element | null {
 
     trackSetupScriptPromptExposure({
       repoId: activeRepo.id,
+      repoHostIdentity: activeRepoHostIdentity,
       promptState,
       trackedPromptKeys: trackedPromptKeysRef.current
     })
-  }, [activeRepo, isDismissed, promptState, sidebarOpen])
+  }, [activeRepo, activeRepoHostIdentity, isDismissed, promptState, sidebarOpen])
 
   const handleConfigure = useCallback(() => {
     if (!activeRepo) {
@@ -143,6 +148,7 @@ function SetupScriptPromptCard(): React.JSX.Element | null {
     }
     if (
       promptState?.repoId === activeRepo.id &&
+      promptState.repoHostIdentity === activeRepoHostIdentity &&
       promptState.status === 'ok' &&
       !promptState.hasEffectiveSetup
     ) {
@@ -156,12 +162,13 @@ function SetupScriptPromptCard(): React.JSX.Element | null {
       )
     }
     openLocalCommandSettings(activeRepo.id)
-  }, [activeRepo, openLocalCommandSettings, promptState])
+  }, [activeRepo, activeRepoHostIdentity, openLocalCommandSettings, promptState])
 
   const handleDismiss = useCallback(() => {
-    if (activeRepo) {
+    if (activeRepo && activeRepoHostIdentity) {
       if (
         promptState?.repoId === activeRepo.id &&
+        promptState.repoHostIdentity === activeRepoHostIdentity &&
         promptState.status === 'ok' &&
         !promptState.hasEffectiveSetup
       ) {
@@ -174,9 +181,9 @@ function SetupScriptPromptCard(): React.JSX.Element | null {
           })
         )
       }
-      dismissSetupScriptPrompt(activeRepo.id)
+      dismissSetupScriptPrompt(activeRepoHostIdentity)
     }
-  }, [activeRepo, dismissSetupScriptPrompt, promptState])
+  }, [activeRepo, activeRepoHostIdentity, dismissSetupScriptPrompt, promptState])
 
   const saveSetupCandidate = useCallback(
     async (input: {
@@ -189,11 +196,17 @@ function SetupScriptPromptCard(): React.JSX.Element | null {
       if (!activeRepo) {
         return
       }
-      setIsImporting(true)
+      const importedRepoHostIdentity = getRepoHostIdentity(activeRepo)
+      const importedHostId = getRepoExecutionHostId(activeRepo)
+      setImportingRepoHostIdentity(importedRepoHostIdentity)
       try {
         const importedRepoId = activeRepo.id
         const nextSettings = buildImportedHookSettings(activeRepo, candidate, hasSharedHooks)
-        const didUpdate = await updateRepo(activeRepo.id, { hookSettings: nextSettings })
+        const didUpdate = await updateRepo(
+          activeRepo.id,
+          { hookSettings: nextSettings },
+          { hostId: importedHostId }
+        )
         if (!didUpdate) {
           track(
             'setup_script_prompt_action',
@@ -232,9 +245,7 @@ function SetupScriptPromptCard(): React.JSX.Element | null {
         if (actionPrefix === 'save_detected_setup') {
           if (mountedRef.current) {
             setPromptState((current) =>
-              current?.repoId === activeRepo.id && current.status === 'ok'
-                ? { ...current, hasEffectiveSetup: true }
-                : current
+              markSetupScriptPromptSaved(current, importedRepoHostIdentity)
             )
             showSavedInProjectSettingsToast({
               onOpenSettings: () => openLocalCommandSettings(importedRepoId),
@@ -247,11 +258,7 @@ function SetupScriptPromptCard(): React.JSX.Element | null {
           return
         }
         if (mountedRef.current) {
-          setPromptState((current) =>
-            current?.repoId === activeRepo.id && current.status === 'ok'
-              ? { ...current, hasEffectiveSetup: true }
-              : current
-          )
+          setPromptState((current) => markSetupScriptPromptSaved(current, importedRepoHostIdentity))
           const skippedCount = candidate.unsupportedFields?.length ?? 0
           showSavedInProjectSettingsToast({
             onOpenSettings: () => openLocalCommandSettings(importedRepoId),
@@ -285,7 +292,9 @@ function SetupScriptPromptCard(): React.JSX.Element | null {
         }
       } finally {
         if (mountedRef.current) {
-          setIsImporting(false)
+          setImportingRepoHostIdentity((current) =>
+            current === importedRepoHostIdentity ? null : current
+          )
         }
       }
     },
@@ -334,20 +343,23 @@ function SetupScriptPromptCard(): React.JSX.Element | null {
     })
   }, [activeRepo, detectedSetupDraft, promptState, saveSetupCandidate])
 
-  if (!sidebarOpen || !activeRepo || !isGitRepoKind(activeRepo) || isDismissed) {
+  if (
+    !sidebarOpen ||
+    !activeRepo ||
+    !activeRepoHostIdentity ||
+    !isGitRepoKind(activeRepo) ||
+    isDismissed
+  ) {
     lastVisiblePromptRef.current = null
     return null
   }
 
-  const activeRepoHostIdentity = getRepoHostIdentity(activeRepo)
-  const renderedPromptState =
-    activeRepo &&
-    getRenderedSetupScriptPromptState({
-      promptState,
-      activeRepoId: activeRepo.id,
-      activeRepoHostIdentity,
-      lastVisiblePrompt: lastVisiblePromptRef.current
-    })
+  const renderedPromptState = getRenderedSetupScriptPromptState({
+    promptState,
+    activeRepoId: activeRepo.id,
+    activeRepoHostIdentity,
+    lastVisiblePrompt: lastVisiblePromptRef.current
+  })
 
   if (
     !renderedPromptState ||
@@ -398,7 +410,7 @@ function SetupScriptPromptCard(): React.JSX.Element | null {
       candidateSource={candidateSource}
       candidateProvenance={candidateProvenance}
       detectedSetupDraft={detectedSetupDraft}
-      isImporting={isImporting}
+      isImporting={importingRepoHostIdentity === activeRepoHostIdentity}
       renderedStateOk={renderedPromptState.status === 'ok'}
       onDismiss={handleDismiss}
       onRetryInspection={handleRetryInspection}
diff --git a/src/renderer/src/components/sidebar/setup-script-prompt-exposure-telemetry.ts b/src/renderer/src/components/sidebar/setup-script-prompt-exposure-telemetry.ts
index 1f62941d592..a4f7028b19b 100644
--- a/src/renderer/src/components/sidebar/setup-script-prompt-exposure-telemetry.ts
+++ b/src/renderer/src/components/sidebar/setup-script-prompt-exposure-telemetry.ts
@@ -1,15 +1,17 @@
 import { track } from '@/lib/telemetry'
-import type { SetupScriptPromptInspection } from '@/lib/setup-script-prompt'
 import { buildSetupScriptPromptTelemetry } from '../../../../shared/setup-script-telemetry'
+import type { SetupScriptPromptState } from './setup-script-prompt-render-state'
 
 export function trackSetupScriptPromptExposure(input: {
   repoId: string
-  promptState: SetupScriptPromptInspection | null
+  repoHostIdentity: string
+  promptState: SetupScriptPromptState | null
   trackedPromptKeys: Set<string>
 }): void {
-  const { promptState, repoId, trackedPromptKeys } = input
+  const { promptState, repoHostIdentity, repoId, trackedPromptKeys } = input
   if (
     promptState?.repoId !== repoId ||
+    promptState.repoHostIdentity !== repoHostIdentity ||
     promptState.status !== 'ok' ||
     promptState.hasEffectiveSetup
   ) {
@@ -23,7 +25,7 @@ export function trackSetupScriptPromptExposure(input: {
   // Why: React may re-render the sidebar often; this event should represent
   // a distinct prompt exposure for this repo/source, not render churn.
   const promptKey = [
-    repoId,
+    repoHostIdentity,
     telemetry.mode,
     telemetry.provider ?? 'none',
     telemetry.file_count_bucket,
diff --git a/src/renderer/src/components/sidebar/setup-script-prompt-render-state.ts b/src/renderer/src/components/sidebar/setup-script-prompt-render-state.ts
index dc693a317a5..0b9d600c4d5 100644
--- a/src/renderer/src/components/sidebar/setup-script-prompt-render-state.ts
+++ b/src/renderer/src/components/sidebar/setup-script-prompt-render-state.ts
@@ -8,6 +8,15 @@ export type LastVisibleSetupScriptPrompt = {
   state: SetupScriptPromptState
 }
 
+export function markSetupScriptPromptSaved(
+  current: SetupScriptPromptState | null,
+  savedRepoHostIdentity: string
+): SetupScriptPromptState | null {
+  return current?.repoHostIdentity === savedRepoHostIdentity && current.status === 'ok'
+    ? { ...current, hasEffectiveSetup: true }
+    : current
+}
+
 export function getRenderedSetupScriptPromptState(input: {
   promptState: SetupScriptPromptState | null
   activeRepoId: string
diff --git a/src/renderer/src/components/sidebar/useSetupScriptPromptRevalidation.test.tsx b/src/renderer/src/components/sidebar/useSetupScriptPromptRevalidation.test.tsx
index 4d7d09bbd8d..6ea400b5bd8 100644
--- a/src/renderer/src/components/sidebar/useSetupScriptPromptRevalidation.test.tsx
+++ b/src/renderer/src/components/sidebar/useSetupScriptPromptRevalidation.test.tsx
@@ -4,25 +4,34 @@ import { act } from 'react'
 import { createRoot, type Root } from 'react-dom/client'
 import { afterEach, beforeEach, describe, expect, it, vi } from 'vitest'
 import { useAppStore } from '@/store'
-import type { SetupScriptPromptInspection } from '@/lib/setup-script-prompt'
 import type { Repo } from '../../../../shared/types'
 import { useSetupScriptPromptRevalidation } from './useSetupScriptPromptRevalidation'
+import type { SetupScriptPromptState } from './setup-script-prompt-render-state'
+import { getRepoHostIdentityForParts } from '@/store/slices/repo-host-identity'
 
 const GIT_REPO = { id: 'repo-1', kind: 'git' } as unknown as Repo
+type OkSetupScriptPromptState = Extract<SetupScriptPromptState, { status: 'ok' }>
 
-function missingSetup(repoId: string): SetupScriptPromptInspection {
-  return { status: 'ok', repoId, hasEffectiveSetup: false, hasSharedHooks: true, candidate: null }
+function missingSetup(repoId: string, hostId = 'local'): OkSetupScriptPromptState {
+  return {
+    status: 'ok',
+    repoId,
+    repoHostIdentity: getRepoHostIdentityForParts(repoId, hostId),
+    hasEffectiveSetup: false,
+    hasSharedHooks: true,
+    candidate: null
+  }
 }
 
-function effectiveSetup(repoId: string): SetupScriptPromptInspection {
-  return { status: 'ok', repoId, hasEffectiveSetup: true, hasSharedHooks: true, candidate: null }
+function effectiveSetup(repoId: string): OkSetupScriptPromptState {
+  return { ...missingSetup(repoId), hasEffectiveSetup: true }
 }
 
 type HarnessProps = {
   activeRepo: Repo | null
   isDismissed: boolean
   sidebarOpen: boolean
-  promptState: SetupScriptPromptInspection | null
+  promptState: SetupScriptPromptState | null
   requestRevalidation: () => void
 }
 
@@ -117,6 +126,22 @@ describe('useSetupScriptPromptRevalidation', () => {
     expect(requestRevalidation).not.toHaveBeenCalled()
   })
 
+  it('does not re-inspect when prompt state belongs to another host with the same repo id', async () => {
+    const requestRevalidation = vi.fn()
+    await render({
+      activeRepo: GIT_REPO,
+      isDismissed: false,
+      sidebarOpen: true,
+      promptState: missingSetup('repo-1', 'runtime:windows'),
+      requestRevalidation
+    })
+
+    await dispatchWindowFocus()
+    await setActiveWorktree('worktree-2')
+
+    expect(requestRevalidation).not.toHaveBeenCalled()
+  })
+
   it('re-inspects when a worktree activates while the prompt shows no effective setup', async () => {
     const requestRevalidation = vi.fn()
     // Mirror the card's real lifecycle: promptState is null on mount, so the
diff --git a/src/renderer/src/components/sidebar/useSetupScriptPromptRevalidation.ts b/src/renderer/src/components/sidebar/useSetupScriptPromptRevalidation.ts
index edeacf09cde..04f9dbcab90 100644
--- a/src/renderer/src/components/sidebar/useSetupScriptPromptRevalidation.ts
+++ b/src/renderer/src/components/sidebar/useSetupScriptPromptRevalidation.ts
@@ -1,8 +1,9 @@
 import { useEffect, useRef } from 'react'
 import { useAppStore } from '@/store'
-import type { SetupScriptPromptInspection } from '@/lib/setup-script-prompt'
 import { isGitRepoKind } from '../../../../shared/repo-kind'
 import type { Repo } from '../../../../shared/types'
+import { getRepoHostIdentity } from '@/store/slices/repo-host-identity'
+import type { SetupScriptPromptState } from './setup-script-prompt-render-state'
 
 /**
  * Re-runs the setup-script prompt inspection when a shared `orca.yaml` setup hook
@@ -13,7 +14,7 @@ export function useSetupScriptPromptRevalidation(input: {
   activeRepo: Repo | null
   isDismissed: boolean
   sidebarOpen: boolean
-  promptState: SetupScriptPromptInspection | null
+  promptState: SetupScriptPromptState | null
   requestRevalidation: () => void
 }): void {
   const { activeRepo, isDismissed, sidebarOpen, promptState, requestRevalidation } = input
@@ -25,6 +26,7 @@ export function useSetupScriptPromptRevalidation(input: {
   const showsMissingSetup =
     promptState?.status === 'ok' &&
     promptState.repoId === activeRepo?.id &&
+    Boolean(activeRepo && promptState.repoHostIdentity === getRepoHostIdentity(activeRepo)) &&
     !promptState.hasEffectiveSetup
 
   // Why: orca.yaml is edited on disk or the hook runs in a terminal outside React
diff --git a/src/renderer/src/lib/setup-script-prompt.test.ts b/src/renderer/src/lib/setup-script-prompt.test.ts
index e592856324e..70d226bc0cf 100644
--- a/src/renderer/src/lib/setup-script-prompt.test.ts
+++ b/src/renderer/src/lib/setup-script-prompt.test.ts
@@ -1,6 +1,7 @@
 import { describe, expect, it, vi } from 'vitest'
 import type { SetupScriptImportCandidate } from '../../../shared/setup-script-imports'
 import type { Repo } from '../../../shared/types'
+import { getRepoHostIdentityForParts } from '@/store/slices/repo-host-identity'
 import {
   buildImportedHookSettings,
   filterSetupScriptPromptDismissalsToValidRepos,
@@ -177,24 +178,51 @@ describe('setup script prompt inspection', () => {
   })
 
   it('ignores legacy prompt dismissals and honors the generation prompt version', () => {
-    expect(isSetupScriptPromptDismissed('repo-1', ['repo-1'])).toBe(false)
+    const localIdentity = getRepoHostIdentityForParts('repo-1', 'local')
+    expect(isSetupScriptPromptDismissed(localIdentity, ['repo-1'])).toBe(false)
     expect(
-      isSetupScriptPromptDismissed('repo-1', [getSetupScriptPromptDismissalKey('repo-1')])
+      isSetupScriptPromptDismissed(localIdentity, [getSetupScriptPromptDismissalKey(localIdentity)])
     ).toBe(true)
   })
 
-  it('keeps only current-version prompt dismissals for valid repos', () => {
+  it('keeps prompt dismissals only for valid repo hosts and migrates unambiguous repo ids', () => {
+    const localIdentity = getRepoHostIdentityForParts('repo-1', 'local')
+    const remoteIdentity = getRepoHostIdentityForParts('repo-1', 'runtime:windows')
     expect(
       filterSetupScriptPromptDismissalsToValidRepos(
         [
           'repo-1',
           getSetupScriptPromptDismissalKey('repo-1'),
-          getSetupScriptPromptDismissalKey('repo-1'),
-          getSetupScriptPromptDismissalKey('repo-2')
+          getSetupScriptPromptDismissalKey(localIdentity),
+          getSetupScriptPromptDismissalKey(localIdentity),
+          getSetupScriptPromptDismissalKey(remoteIdentity)
         ],
-        new Set(['repo-1'])
+        new Set([localIdentity])
       )
-    ).toEqual([getSetupScriptPromptDismissalKey('repo-1')])
+    ).toEqual([getSetupScriptPromptDismissalKey(localIdentity)])
+  })
+
+  it('drops a legacy repo-id dismissal when that id exists on multiple hosts', () => {
+    const localIdentity = getRepoHostIdentityForParts('repo-1', 'local')
+    const remoteIdentity = getRepoHostIdentityForParts('repo-1', 'runtime:windows')
+
+    expect(
+      filterSetupScriptPromptDismissalsToValidRepos(
+        [getSetupScriptPromptDismissalKey('repo-1')],
+        new Set([localIdentity, remoteIdentity])
+      )
+    ).toEqual([])
+  })
+
+  it('does not reuse a setup prompt dismissal on another host with the same repo id', () => {
+    const localIdentity = getRepoHostIdentityForParts('repo-1', 'local')
+    const remoteIdentity = getRepoHostIdentityForParts('repo-1', 'runtime:windows')
+
+    expect(
+      isSetupScriptPromptDismissed(remoteIdentity, [
+        getSetupScriptPromptDismissalKey(localIdentity)
+      ])
+    ).toBe(false)
   })
 
   it('formats setup candidate provenance for sidebar review copy', () => {
diff --git a/src/renderer/src/lib/setup-script-prompt.ts b/src/renderer/src/lib/setup-script-prompt.ts
index e60e3eaa7dd..d85a3a9ec30 100644
--- a/src/renderer/src/lib/setup-script-prompt.ts
+++ b/src/renderer/src/lib/setup-script-prompt.ts
@@ -97,25 +97,45 @@ export function ignoresSharedSetupScripts(repo: Pick<Repo, 'hookSettings'>): boo
   )
 }
 
-export function getSetupScriptPromptDismissalKey(repoId: string): string {
-  return `${SETUP_SCRIPT_PROMPT_DISMISSAL_PREFIX}${repoId}`
+export function getSetupScriptPromptDismissalKey(repoHostIdentity: string): string {
+  return `${SETUP_SCRIPT_PROMPT_DISMISSAL_PREFIX}${repoHostIdentity}`
 }
 
 export function isSetupScriptPromptDismissed(
-  repoId: string,
+  repoHostIdentity: string,
   dismissedEntries: readonly string[]
 ): boolean {
-  return dismissedEntries.includes(getSetupScriptPromptDismissalKey(repoId))
+  return dismissedEntries.includes(getSetupScriptPromptDismissalKey(repoHostIdentity))
 }
 
 export function filterSetupScriptPromptDismissalsToValidRepos(
   value: unknown,
-  validRepoIds: Set<string>
+  validRepoHostIdentities: Set<string>
 ): string[] {
-  return sanitizeSetupScriptPromptDismissals(value).filter((entry) => {
-    const repoId = entry.slice(SETUP_SCRIPT_PROMPT_DISMISSAL_PREFIX.length)
-    return validRepoIds.has(repoId)
-  })
+  const unambiguousIdentityByRepoId = new Map<string, string | null>()
+  for (const identity of validRepoHostIdentities) {
+    const separatorIndex = identity.indexOf('\0')
+    const repoId = separatorIndex >= 0 ? identity.slice(separatorIndex + 1) : identity
+    unambiguousIdentityByRepoId.set(
+      repoId,
+      unambiguousIdentityByRepoId.has(repoId) ? null : identity
+    )
+  }
+
+  const next: string[] = []
+  for (const entry of sanitizeSetupScriptPromptDismissals(value)) {
+    const repoHostIdentity = entry.slice(SETUP_SCRIPT_PROMPT_DISMISSAL_PREFIX.length)
+    const validIdentity = validRepoHostIdentities.has(repoHostIdentity)
+      ? repoHostIdentity
+      : unambiguousIdentityByRepoId.get(repoHostIdentity)
+    if (validIdentity) {
+      const validEntry = getSetupScriptPromptDismissalKey(validIdentity)
+      if (!next.includes(validEntry)) {
+        next.push(validEntry)
+      }
+    }
+  }
+  return next
 }
 
 export function sanitizeSetupScriptPromptDismissals(value: unknown): string[] {
diff --git a/src/renderer/src/store/slices/repos-all-hosts.test.ts b/src/renderer/src/store/slices/repos-all-hosts.test.ts
index f77e4db2b1e..638941df094 100644
--- a/src/renderer/src/store/slices/repos-all-hosts.test.ts
+++ b/src/renderer/src/store/slices/repos-all-hosts.test.ts
@@ -785,8 +785,8 @@ describe('fetchReposForAllHosts', () => {
 
   it('preserves remote repo filters during first-paint local catalog refresh', async () => {
     const store = createTestStore()
-    const remoteDismissalKey = getSetupScriptPromptDismissalKey('remote-repo')
-    const staleDismissalKey = getSetupScriptPromptDismissalKey('stale-repo')
+    const remoteDismissalKey = getSetupScriptPromptDismissalKey('runtime:env-1\0remote-repo')
+    const staleDismissalKey = getSetupScriptPromptDismissalKey('local\0stale-repo')
     store.setState({
       activeRepoId: 'remote-repo',
       filterRepoIds: ['remote-repo', 'stale-repo'],
diff --git a/src/renderer/src/store/slices/repos-setup-script-dismissals.test.ts b/src/renderer/src/store/slices/repos-setup-script-dismissals.test.ts
index 4dc22196f7f..f805b66ac0c 100644
--- a/src/renderer/src/store/slices/repos-setup-script-dismissals.test.ts
+++ b/src/renderer/src/store/slices/repos-setup-script-dismissals.test.ts
@@ -2,6 +2,7 @@ import { beforeEach, describe, expect, it, vi } from 'vitest'
 import type { Repo } from '../../../../shared/types'
 import { getSetupScriptPromptDismissalKey } from '../../lib/setup-script-prompt'
 import { createTestStore } from './store-test-helpers'
+import { getRepoHostIdentityForParts } from './repo-host-identity'
 
 const localRepo: Repo = {
   id: 'local-repo',
@@ -27,19 +28,20 @@ beforeEach(() => {
 describe('repo setup script prompt dismissals', () => {
   it('keeps only current setup prompt dismissals for fetched repos', async () => {
     reposList.mockResolvedValue([localRepo])
+    const localIdentity = getRepoHostIdentityForParts(localRepo.id, 'local')
     const store = createTestStore()
     store.setState({
       setupScriptPromptDismissedRepoIds: [
         localRepo.id,
-        getSetupScriptPromptDismissalKey(localRepo.id),
-        getSetupScriptPromptDismissalKey('stale-repo')
+        getSetupScriptPromptDismissalKey(localIdentity),
+        getSetupScriptPromptDismissalKey(getRepoHostIdentityForParts('stale-repo', 'local'))
       ]
     })
 
     await store.getState().fetchRepos()
 
     expect(store.getState().setupScriptPromptDismissedRepoIds).toEqual([
-      getSetupScriptPromptDismissalKey(localRepo.id)
+      getSetupScriptPromptDismissalKey(localIdentity)
     ])
   })
 })
diff --git a/src/renderer/src/store/slices/repos.ts b/src/renderer/src/store/slices/repos.ts
index 8544817d07a..82ec1e26d59 100644
--- a/src/renderer/src/store/slices/repos.ts
+++ b/src/renderer/src/store/slices/repos.ts
@@ -1691,6 +1691,7 @@ export const createRepoSlice: StateCreator<AppState, [], [], RepoSlice> = (set,
         const reconciliation = reconcileSupersededSshRepos(result.repos, s)
         const prunedRepos = applyManualRepoOrder(reconciliation.repos, s.manualRepoOrder)
         const validRepoIds = new Set(prunedRepos.map((repo) => repo.id))
+        const validRepoHostIdentities = new Set(prunedRepos.map(getRepoHostIdentity))
         const projectCompatibility = projectCompatibilityForReconciledRepos(
           prunedRepos,
           catalog.projectHostSetupCompatibility
@@ -1721,7 +1722,7 @@ export const createRepoSlice: StateCreator<AppState, [], [], RepoSlice> = (set,
           filterRepoIds: s.filterRepoIds.filter((projectId) => validRepoIds.has(projectId)),
           setupScriptPromptDismissedRepoIds: filterSetupScriptPromptDismissalsToValidRepos(
             s.setupScriptPromptDismissedRepoIds,
-            validRepoIds
+            validRepoHostIdentities
           )
         }
       })
@@ -1763,6 +1764,7 @@ export const createRepoSlice: StateCreator<AppState, [], [], RepoSlice> = (set,
         const reconciliation = reconcileSupersededSshRepos(result.repos, s)
         const finalizedRepos = applyManualRepoOrder(reconciliation.repos, s.manualRepoOrder)
         const validRepoIds = new Set(finalizedRepos.map((repo) => repo.id))
+        const validRepoHostIdentities = new Set(finalizedRepos.map(getRepoHostIdentity))
         const projectCompatibility = projectCompatibilityForReconciledRepos(
           finalizedRepos,
           catalog.projectHostSetupCompatibility
@@ -1792,7 +1794,7 @@ export const createRepoSlice: StateCreator<AppState, [], [], RepoSlice> = (set,
           filterRepoIds: s.filterRepoIds.filter((projectId) => validRepoIds.has(projectId)),
           setupScriptPromptDismissedRepoIds: filterSetupScriptPromptDismissalsToValidRepos(
             s.setupScriptPromptDismissedRepoIds,
-            validRepoIds
+            validRepoHostIdentities
           )
         }
       })
@@ -1860,12 +1862,13 @@ export const createRepoSlice: StateCreator<AppState, [], [], RepoSlice> = (set,
     const validateRepoScopedUi = (): void => {
       set((s) => {
         const validRepoIds = new Set(s.repos.map((repo) => repo.id))
+        const validRepoHostIdentities = new Set(s.repos.map(getRepoHostIdentity))
         return {
           activeRepoId: s.activeRepoId && validRepoIds.has(s.activeRepoId) ? s.activeRepoId : null,
           filterRepoIds: s.filterRepoIds.filter((projectId) => validRepoIds.has(projectId)),
           setupScriptPromptDismissedRepoIds: filterSetupScriptPromptDismissalsToValidRepos(
             s.setupScriptPromptDismissedRepoIds,
-            validRepoIds
+            validRepoHostIdentities
           ),
           trustedOrcaHooks: filterTrustedOrcaHooksToValidRepos(s.trustedOrcaHooks, validRepoIds)
         }
diff --git a/src/renderer/src/store/slices/ui.test.ts b/src/renderer/src/store/slices/ui.test.ts
index 4b7169cbe3b..10df98636b1 100644
--- a/src/renderer/src/store/slices/ui.test.ts
+++ b/src/renderer/src/store/slices/ui.test.ts
@@ -23,6 +23,7 @@ import { buildAgentNotificationId } from '../../../../shared/agent-notification-
 import type { AgentStatusEntry } from '../../../../shared/agent-status-types'
 import type { TaskSourceContext } from '../../../../shared/task-source-context'
 import { getSetupScriptPromptDismissalKey } from '../../lib/setup-script-prompt'
+import { getRepoHostIdentityForParts } from './repo-host-identity'
 
 const mocks = vi.hoisted(() => ({
   sendNotesToActiveAgentSession: vi.fn(),
@@ -860,7 +861,9 @@ describe('createUISlice hydratePersistedUI', () => {
 
   it('preserves persisted repo filters until repos are loaded', () => {
     const store = createUIStore()
-    const remoteDismissalKey = getSetupScriptPromptDismissalKey('remote-repo')
+    const remoteDismissalKey = getSetupScriptPromptDismissalKey(
+      getRepoHostIdentityForParts('remote-repo', 'runtime:env-1')
+    )
 
     store.getState().hydratePersistedUI(
       makePersistedUI({
@@ -882,8 +885,12 @@ describe('createUISlice hydratePersistedUI', () => {
 
   it('validates persisted repo filters when repos are already loaded', () => {
     const store = createUIStore()
-    const localDismissalKey = getSetupScriptPromptDismissalKey('local-repo')
-    const staleDismissalKey = getSetupScriptPromptDismissalKey('stale-repo')
+    const localDismissalKey = getSetupScriptPromptDismissalKey(
+      getRepoHostIdentityForParts('local-repo', 'local')
+    )
+    const staleDismissalKey = getSetupScriptPromptDismissalKey(
+      getRepoHostIdentityForParts('stale-repo', 'local')
+    )
     store.setState({
       repos: [
         { id: 'local-repo', path: '/local', displayName: 'Local', badgeColor: '#000', addedAt: 1 }
diff --git a/src/renderer/src/store/slices/ui.ts b/src/renderer/src/store/slices/ui.ts
index cc81e3ae09b..9197153fde5 100644
--- a/src/renderer/src/store/slices/ui.ts
+++ b/src/renderer/src/store/slices/ui.ts
@@ -128,6 +128,7 @@ import {
 import { buildAgentNotificationId } from '../../../../shared/agent-notification-id'
 import { parsePaneKey } from '../../../../shared/stable-pane-id'
 import { translate } from '@/i18n/i18n'
+import { getRepoHostIdentity } from './repo-host-identity'
 
 export type PendingSidebarWorktreeReveal = {
   worktreeId: string
@@ -828,7 +829,7 @@ export type UISlice = {
   markOrcaHookRepoAlwaysTrusted: (repoId: string) => void
   clearOrcaHookTrustForRepo: (repoId: string) => void
   setupScriptPromptDismissedRepoIds: string[]
-  dismissSetupScriptPrompt: (repoId: string) => void
+  dismissSetupScriptPrompt: (repoHostIdentity: string) => void
   setupGuideSidebarDismissed: boolean
   setSetupGuideSidebarDismissed: (dismissed: boolean) => void
   setupGuideBrowserMilestoneMigrated: boolean
@@ -1885,10 +1886,10 @@ export const createUISlice: StateCreator<AppState, [], [], UISlice> = (set, get)
       return { trustedOrcaHooks: next }
     }),
   setupScriptPromptDismissedRepoIds: [],
-  dismissSetupScriptPrompt: (repoId) =>
+  dismissSetupScriptPrompt: (repoHostIdentity) =>
     set((s) => {
-      const dismissalKey = getSetupScriptPromptDismissalKey(repoId)
-      if (!repoId || s.setupScriptPromptDismissedRepoIds.includes(dismissalKey)) {
+      const dismissalKey = getSetupScriptPromptDismissalKey(repoHostIdentity)
+      if (!repoHostIdentity || s.setupScriptPromptDismissedRepoIds.includes(dismissalKey)) {
         return s
       }
       const next = [...s.setupScriptPromptDismissedRepoIds, dismissalKey]
@@ -2346,6 +2347,7 @@ export const createUISlice: StateCreator<AppState, [], [], UISlice> = (set, get)
       const manualRepoOrder = normalizeManualRepoOrder(ui.manualRepoOrder)
       const orderedRepos = applyManualRepoOrder(s.repos, manualRepoOrder)
       const validRepoIds = new Set(s.repos.map((repo) => repo.id))
+      const validRepoHostIdentities = new Set(s.repos.map(getRepoHostIdentity))
       const persistedFilterRepoIds = sanitizePersistedRepoIds(ui.filterRepoIds)
       // Why: pre-rename builds used sidekick* keys; read as fallback only so new pet* writes win after upgrade.
       const customPets = Array.isArray(ui.customPets)
@@ -2498,11 +2500,11 @@ export const createUISlice: StateCreator<AppState, [], [], UISlice> = (set, get)
             : null,
         trustedOrcaHooks: hydrateTrustedOrcaHooks(ui.trustedOrcaHooks, validRepoIds),
         setupScriptPromptDismissedRepoIds:
-          validRepoIds.size === 0
+          validRepoHostIdentities.size === 0
             ? sanitizeSetupScriptPromptDismissals(ui.setupScriptPromptDismissedRepoIds)
             : filterSetupScriptPromptDismissalsToValidRepos(
                 ui.setupScriptPromptDismissedRepoIds,
-                validRepoIds
+                validRepoHostIdentities
               ),
         setupGuideSidebarDismissed: ui.setupGuideSidebarDismissed === true,
         setupGuideBrowserMilestoneMigrated: ui.setupGuideBrowserMilestoneMigrated === true,