diff --git a/src/main/runtime/rpc/methods/client-ui.test.ts b/src/main/runtime/rpc/methods/client-ui.test.ts
index a1f24c28a9f..15c2def486e 100644
--- a/src/main/runtime/rpc/methods/client-ui.test.ts
+++ b/src/main/runtime/rpc/methods/client-ui.test.ts
@@ -560,13 +560,37 @@ describe('client UI RPC methods', () => {
     }
     const response = await dispatcher.dispatch(makeRequest('ui.set', payload))
 
+    const { manualRepoOrder: _desktopOwnedOrder, ...forwarded } = payload
     expect(runtime.updateUIState).toHaveBeenCalledWith({
-      ...payload,
+      ...forwarded,
       worktreeCardProperties: ['status', 'unread', 'branch', 'automation', 'inline-agents']
     })
     expect(response).toMatchObject({ ok: true, result: { ui: updated } })
   })
 
+  it('drops a paired client manualRepoOrder while forwarding the rest of the payload', async () => {
+    const runtime = {
+      getRuntimeId: () => 'test-runtime',
+      updateUIState: vi.fn(() => getDefaultUIState())
+    } as unknown as OrcaRuntimeService
+    const dispatcher = new RpcDispatcher({ runtime, methods: CLIENT_UI_METHODS })
+
+    // A paired web client restamps every repo onto its own runtime:web-* pseudo-host, so its
+    // overlay names hosts this profile will never own; persisting it erases the desktop order.
+    const response = await dispatcher.dispatch(
+      makeRequest('ui.set', {
+        sidebarWidth: 280,
+        manualRepoOrder: [
+          { hostId: 'runtime:web-11111111-2222-3333-4444-555555555555', repoId: 'repo-a' },
+          { hostId: 'runtime:web-11111111-2222-3333-4444-555555555555', repoId: 'repo-b' }
+        ]
+      })
+    )
+
+    expect(response).toMatchObject({ ok: true })
+    expect(runtime.updateUIState).toHaveBeenCalledWith({ sidebarWidth: 280 })
+  })
+
   // Why one case per field: the schema is strict, so a single unlisted key makes
   // the dispatcher reject the ENTIRE ui.set payload with invalid_argument instead
   // of stripping it. A combined payload would pass as soon as any one field were
diff --git a/src/main/runtime/rpc/methods/client-ui.ts b/src/main/runtime/rpc/methods/client-ui.ts
index 70ad9e9df57..2096843d355 100644
--- a/src/main/runtime/rpc/methods/client-ui.ts
+++ b/src/main/runtime/rpc/methods/client-ui.ts
@@ -55,9 +55,17 @@ export const CLIENT_UI_METHODS: RpcMethod[] = [
   defineMethod({
     name: 'ui.set',
     params: UiUpdate,
+    // Why manualRepoOrder is dropped rather than removed from the schema: a paired client keys
+    // its overlay to its own execution hosts, so forwarding it blind-replaces the desktop's
+    // order. The strict schema still has to accept the field or old clients' whole payload fails.
     handler: (params, { runtime }) => {
-      const { hideWorkspacesFromOtherDevices: _clientLocalFilter, ...hostUpdates } = params
+      const {
+        hideWorkspacesFromOtherDevices: _clientLocalFilter,
+        manualRepoOrder: _desktopOwnedOrder,
+        ...hostUpdates
+      } = params
       void _clientLocalFilter
+      void _desktopOwnedOrder
       return { ui: runtime.updateUIState(hostUpdates as Partial<PersistedUIState>) }
     }
   }),
diff --git a/src/renderer/src/hooks/direct-ssh-host-hydration.test.ts b/src/renderer/src/hooks/direct-ssh-host-hydration.test.ts
index 4aa654cf33a..fba5db317f8 100644
--- a/src/renderer/src/hooks/direct-ssh-host-hydration.test.ts
+++ b/src/renderer/src/hooks/direct-ssh-host-hydration.test.ts
@@ -113,6 +113,32 @@ describe('createDirectSshHostHydration', () => {
     ])
   })
 
+  it('keeps the manual cross-host order when the host catalog is republished', async () => {
+    const owner = authority('box')
+    const store = createStore<AppState>(() =>
+      state({
+        repos: [repo('bravo', 'box'), repo('alpha', null), repo('delta', 'box')],
+        manualRepoOrder: [
+          { hostId: 'ssh:box', repoId: 'bravo' },
+          { hostId: 'local', repoId: 'alpha' },
+          { hostId: 'ssh:box', repoId: 'delta' }
+        ]
+      })
+    )
+    const hydration = createDirectSshHostHydration({
+      store,
+      listRepos: vi.fn(async () =>
+        hostSnapshot(owner, [repo('bravo', 'box'), repo('delta', 'box')])
+      ),
+      listLineage: vi.fn(),
+      isCurrentAuthority: () => true
+    })
+
+    await hydration.capturePreparationInput(owner, 'reconnect')
+
+    expect(store.getState().repos.map((entry) => entry.id)).toEqual(['bravo', 'alpha', 'delta'])
+  })
+
   it('rejects a mismatched host response without publishing', async () => {
     const owner = authority()
     const store = createStore<AppState>(() => state({ repos: [repo('cached', 'target-a')] }))
diff --git a/src/renderer/src/hooks/direct-ssh-host-hydration.ts b/src/renderer/src/hooks/direct-ssh-host-hydration.ts
index 069b3b3d323..419dc134075 100644
--- a/src/renderer/src/hooks/direct-ssh-host-hydration.ts
+++ b/src/renderer/src/hooks/direct-ssh-host-hydration.ts
@@ -2,6 +2,7 @@ import type { StoreApi } from 'zustand'
 import { getRepoExecutionHostId, toSshExecutionHostId } from '../../../shared/execution-host'
 import type { HostLineageSnapshot } from '../../../shared/host-lineage-contract'
 import type { HostRepoCatalogSnapshot } from '../../../shared/host-repo-catalog-contract'
+import { applyManualRepoOrder } from '../../../shared/manual-repo-order'
 import type { DirectSshAuthority } from '../../../shared/ssh-types'
 import { isWorkspaceKey } from '../../../shared/workspace-scope'
 import type { AppState } from '../store/types'
@@ -63,12 +64,14 @@ function mergeExactHostCatalog(state: AppState, snapshot: HostRepoCatalogSnapsho
     return state
   }
   const hostId = snapshot.authority.executionHostId
+  // Why re-apply the overlay: re-appending the host's rows puts them at the tail, which would
+  // undo the user's manual cross-host order on every connect.
   return {
     ...state,
-    repos: [
-      ...state.repos.filter((repo) => getRepoExecutionHostId(repo) !== hostId),
-      ...snapshot.repos
-    ]
+    repos: applyManualRepoOrder(
+      [...state.repos.filter((repo) => getRepoExecutionHostId(repo) !== hostId), ...snapshot.repos],
+      state.manualRepoOrder
+    )
   }
 }
 
diff --git a/src/renderer/src/web/web-preload-api-ui.test.ts b/src/renderer/src/web/web-preload-api-ui.test.ts
index e809210aac1..15ac7f60c16 100644
--- a/src/renderer/src/web/web-preload-api-ui.test.ts
+++ b/src/renderer/src/web/web-preload-api-ui.test.ts
@@ -1,6 +1,7 @@
 import { afterEach, beforeEach, describe, expect, it, vi } from 'vitest'
 import type { FeatureInteractionState } from '../../../shared/feature-interactions'
 import type { RuntimeRpcResponse } from '../../../shared/runtime-rpc-envelope'
+import type { ManualRepoOrderEntry } from '../../../shared/ui-chrome-types'
 import {
   installApi,
   installBrowserGlobals,
@@ -327,6 +328,44 @@ describe('web UI preload API', () => {
     })
   })
 
+  it('keeps the manual repo order browser-local instead of overwriting the host order', async () => {
+    const runtimeCalls: { method: string; params: unknown }[] = []
+    vi.doMock('./web-runtime-client', () => ({
+      WebRuntimeClient: class {
+        call(method: string, params?: unknown): Promise<RuntimeRpcResponse<unknown>> {
+          runtimeCalls.push({ method, params })
+          return Promise.resolve({
+            id: method,
+            ok: true,
+            result: { ui: {} },
+            _meta: { runtimeId: 'runtime-1' }
+          })
+        }
+
+        close(): void {}
+      }
+    }))
+
+    const globals = installBrowserGlobals('Linux')
+    writeStoredRuntimeEnvironment(globals.storage)
+    const { installWebPreloadApi } = await import('./web-preload-api')
+    installWebPreloadApi()
+
+    // The web client keys its order to its own runtime:web-* host, so a host that predates the
+    // RPC-side strip would persist it over the desktop's local/ssh-keyed order.
+    const manualRepoOrder: ManualRepoOrderEntry[] = [
+      { hostId: 'runtime:web-11111111-2222-3333-4444-555555555555', repoId: 'repo-b' },
+      { hostId: 'runtime:web-11111111-2222-3333-4444-555555555555', repoId: 'repo-a' }
+    ]
+    await globals.window.api.ui.set({ manualRepoOrder, sidebarWidth: 280 })
+
+    expect(runtimeCalls[0]).toEqual({ method: 'ui.set', params: { sidebarWidth: 280 } })
+    expect(JSON.parse(globals.storage.getItem('orca.web.ui.v1') ?? '{}')).toMatchObject({
+      manualRepoOrder,
+      sidebarWidth: 280
+    })
+  })
+
   it('union-merges local contextual tour seen ids when ui.get returns stale host state', async () => {
     vi.doMock('./web-runtime-client', () => ({
       WebRuntimeClient: class {
diff --git a/src/renderer/src/web/web-preload-api.ts b/src/renderer/src/web/web-preload-api.ts
index 57f5efacef3..3b191594d33 100644
--- a/src/renderer/src/web/web-preload-api.ts
+++ b/src/renderer/src/web/web-preload-api.ts
@@ -2731,9 +2731,15 @@ function createWebUiApi(): NonNullable<Partial<PreloadApi>['ui']> {
       const next = mergeWebUIState(readLocalWebUIState(), updates)
       writeJson(UI_STORAGE_KEY, next)
       zoomLevel = next.uiZoomLevel
-      const { hideWorkspacesFromOtherDevices: _clientLocalWorkspaceFilter, ...hostUpdates } =
-        updates
+      // Why manualRepoOrder stays local: it is keyed to this client's runtime:web-* hosts, so
+      // sending it would overwrite the desktop profile's order on hosts that predate the strip.
+      const {
+        hideWorkspacesFromOtherDevices: _clientLocalWorkspaceFilter,
+        manualRepoOrder: _desktopOwnedOrder,
+        ...hostUpdates
+      } = updates
       void _clientLocalWorkspaceFilter
+      void _desktopOwnedOrder
       try {
         await callRuntimeResult('ui.set', hostUpdates, 15_000)
       } catch {