diff --git a/src/renderer/src/components/sidebar/WorktreeList.tsx b/src/renderer/src/components/sidebar/WorktreeList.tsx
index 73726d09ae0..df2250c3c0f 100644
--- a/src/renderer/src/components/sidebar/WorktreeList.tsx
+++ b/src/renderer/src/components/sidebar/WorktreeList.tsx
@@ -142,7 +142,10 @@ import {
   type ScrollToCurrentWorkspaceRevealRequestDetail
 } from '@/lib/scroll-to-current-workspace-status'
 import { isRepoHeaderActionTarget, useRepoHeaderDrag } from './project-header-drag'
-import { getSidebarOrderedRepoHeaderIdsByBucket } from './project-header-drop'
+import {
+  getLogicalRepoOrderRankById,
+  getSidebarOrderedRepoHeaderIdsByBucket
+} from './project-header-drop'
 import { useProjectGroupHeaderDrag } from './project-group-header-drag'
 import { getSidebarOrderedProjectGroupHeaderIdsByBucket } from './project-group-header-drop'
 import {
@@ -5686,9 +5689,7 @@ const WorktreeList = React.memo(function WorktreeList({
     })
   }, [defaultHostId, folderWorkspaces, projectGroups, visibleHostIdSet])
   const repoOrder = useMemo(() => {
-    const map = new Map<string, number>()
-    repos.forEach((r, i) => map.set(r.id, i))
-    return map
+    return getLogicalRepoOrderRankById(repos.map((repo) => repo.id))
   }, [repos])
   const [importedWorktreeCardActionState, setImportedWorktreeCardActionState] = useState<
     Map<string, ImportedWorktreeCardActionState>
diff --git a/src/renderer/src/components/sidebar/project-header-drag-commit.test.ts b/src/renderer/src/components/sidebar/project-header-drag-commit.test.ts
index 70a40d6d250..a988db5bd3d 100644
--- a/src/renderer/src/components/sidebar/project-header-drag-commit.test.ts
+++ b/src/renderer/src/components/sidebar/project-header-drag-commit.test.ts
@@ -53,6 +53,24 @@ describe('commitProjectHeaderDragDrop', () => {
     expect(onCommitRepoOrder).toHaveBeenCalledWith(['c', 'a', 'b'])
   })
 
+  it('moves a merged paired-host header upward as one stable block', () => {
+    const onCommitRepoOrder = vi.fn()
+    const repos = [makeRepo('b'), makeRepo('same'), makeRepo('c')]
+    const repoById = new Map(repos.map((repo) => [repo.id, repo]))
+
+    commitProjectHeaderDragDrop({
+      session: makeSession('same', ['b', 'same', 'c']),
+      sidebarDropIndex: 0,
+      orderedRepoIds: ['b', 'same', 'c', 'same'],
+      repoById,
+      usesProjectGroupOrdering: false,
+      onCommitRepoOrder,
+      onCommitProjectGroupOrder: vi.fn()
+    })
+
+    expect(onCommitRepoOrder).toHaveBeenCalledWith(['same', 'same', 'b', 'c'])
+  })
+
   it('commits projectGroupOrder when project groups are present', () => {
     const onCommitProjectGroupOrder = vi.fn()
     const repos = [
diff --git a/src/renderer/src/components/sidebar/project-header-drag-commit.ts b/src/renderer/src/components/sidebar/project-header-drag-commit.ts
index 43c513905a6..57cc5c63a09 100644
--- a/src/renderer/src/components/sidebar/project-header-drag-commit.ts
+++ b/src/renderer/src/components/sidebar/project-header-drag-commit.ts
@@ -1,5 +1,6 @@
 import {
   applyAllRepoInsertAt,
+  getLogicalRepoOrderRankById,
   getProjectGroupOrderForSidebarDrop,
   mapSidebarProjectHeaderDropIndexToSiblingInsertIndex,
   mapSidebarRepoDropIndexToAllRepoInsertAt
@@ -46,9 +47,7 @@ export function commitProjectHeaderDragDrop(args: {
     if (siblingDropIndex === sourceIndexInSiblings) {
       return
     }
-    const repoOrderRankById = new Map(
-      args.orderedRepoIds.map((repoId, index) => [repoId, index] as const)
-    )
+    const repoOrderRankById = getLogicalRepoOrderRankById(args.orderedRepoIds)
     const order = getProjectGroupOrderForSidebarDrop({
       siblings,
       dropIndex: siblingDropIndex,
diff --git a/src/renderer/src/components/sidebar/project-header-drop.test.ts b/src/renderer/src/components/sidebar/project-header-drop.test.ts
index dee5572e02f..c0382a5f162 100644
--- a/src/renderer/src/components/sidebar/project-header-drop.test.ts
+++ b/src/renderer/src/components/sidebar/project-header-drop.test.ts
@@ -4,6 +4,7 @@ import { describe, expect, it } from 'vitest'
 import {
   applyAllRepoInsertAt,
   computeProjectHeaderDropPreview,
+  getLogicalRepoOrderRankById,
   getProjectGroupOrderForSidebarDrop,
   getProjectHeaderDragBucketKey,
   getSidebarOrderedRepoHeaderIdsByBucket,
@@ -53,6 +54,20 @@ describe('getSidebarOrderedRepoHeaderIdsByBucket', () => {
   })
 })
 
+describe('getLogicalRepoOrderRankById', () => {
+  it('anchors a merged paired-host header to its first persisted occurrence', () => {
+    const rankById = getLogicalRepoOrderRankById(['b', 'same', 'c', 'same'])
+
+    expect(rankById).toEqual(
+      new Map([
+        ['b', 0],
+        ['same', 1],
+        ['c', 2]
+      ])
+    )
+  })
+})
+
 describe('mapSidebarRepoDropIndexToAllRepoInsertAt', () => {
   const sidebar = ['a', 'b', 'c']
 
@@ -320,6 +335,15 @@ describe('applyAllRepoInsertAt', () => {
     ])
   })
 
+  it('moves duplicate host occurrences as one stable logical-project block', () => {
+    expect(applyAllRepoInsertAt(['b', 'same', 'c', 'same'], 'same', 0)).toEqual([
+      'same',
+      'same',
+      'b',
+      'c'
+    ])
+  })
+
   it('returns null for no-op reorders', () => {
     expect(applyAllRepoInsertAt(['a', 'b', 'c'], 'b', 2)).toBeNull()
   })
diff --git a/src/renderer/src/components/sidebar/project-header-drop.ts b/src/renderer/src/components/sidebar/project-header-drop.ts
index 00b7169b97e..be012eb72ce 100644
--- a/src/renderer/src/components/sidebar/project-header-drop.ts
+++ b/src/renderer/src/components/sidebar/project-header-drop.ts
@@ -54,6 +54,20 @@ export function getSidebarOrderedRepoHeaderIdsByBucket(
   return buckets
 }
 
+export function getLogicalRepoOrderRankById(
+  orderedRepoIds: readonly string[]
+): Map<string, number> {
+  const rankById = new Map<string, number>()
+  orderedRepoIds.forEach((repoId, index) => {
+    // Why: paired hosts can contribute the same logical project ID; its merged
+    // header must anchor to the first occurrence instead of whichever host loaded last.
+    if (!rankById.has(repoId)) {
+      rankById.set(repoId, index)
+    }
+  })
+  return rankById
+}
+
 export function getProjectGroupOrderForSidebarDrop(args: {
   siblings: readonly Repo[]
   dropIndex: number
@@ -203,16 +217,20 @@ export function applyAllRepoInsertAt(
   draggedRepoId: string,
   insertAt: number
 ): string[] | null {
-  const fromIndex = allRepoIds.indexOf(draggedRepoId)
-  if (fromIndex === -1 || insertAt < 0 || insertAt > allRepoIds.length) {
+  if (!allRepoIds.includes(draggedRepoId) || insertAt < 0 || insertAt > allRepoIds.length) {
     return null
   }
-  const next = allRepoIds.slice()
-  next.splice(fromIndex, 1)
-  const adjustedInsertAt = insertAt > fromIndex ? insertAt - 1 : insertAt
-  if (adjustedInsertAt === fromIndex) {
+  // Why: one merged header controls every host-qualified occurrence; moving
+  // them together prevents a drag from persisting a cross-host split project.
+  const draggedBlock = allRepoIds.filter((repoId) => repoId === draggedRepoId)
+  const removedBeforeInsert = allRepoIds
+    .slice(0, insertAt)
+    .filter((repoId) => repoId === draggedRepoId).length
+  const adjustedInsertAt = insertAt - removedBeforeInsert
+  const next = allRepoIds.filter((repoId) => repoId !== draggedRepoId)
+  next.splice(adjustedInsertAt, 0, ...draggedBlock)
+  if (next.every((repoId, index) => repoId === allRepoIds[index])) {
     return null
   }
-  next.splice(adjustedInsertAt, 0, draggedRepoId)
   return next
 }
diff --git a/src/renderer/src/store/slices/repos-host-identity-routing.test.ts b/src/renderer/src/store/slices/repos-host-identity-routing.test.ts
index 449290d81f4..23325aa73e9 100644
--- a/src/renderer/src/store/slices/repos-host-identity-routing.test.ts
+++ b/src/renderer/src/store/slices/repos-host-identity-routing.test.ts
@@ -496,6 +496,42 @@ describe('repo slice host identity routing', () => {
     })
   })
 
+  it('persists a moved paired-host project block without reversing its host occurrences', async () => {
+    reposReorderForHost.mockResolvedValue({ status: 'applied' })
+    runtimeEnvironmentCall.mockResolvedValue({
+      id: 'rpc-paired-project-reorder',
+      ok: true,
+      result: { status: 'applied' },
+      _meta: { runtimeId: 'runtime-remote' }
+    })
+    const bravo = { ...localDuplicate, id: 'bravo' }
+    const charlie = { ...remoteDuplicate, id: 'charlie' }
+    const store = createTestStore()
+    store.setState({ repos: [bravo, localDuplicate, charlie, remoteDuplicate] })
+
+    await store.getState().reorderRepos(['same-repo', 'same-repo', 'bravo', 'charlie'])
+
+    expect(store.getState().repos).toEqual([localDuplicate, remoteDuplicate, bravo, charlie])
+    expect(uiSet).toHaveBeenCalledWith({
+      manualRepoOrder: [
+        { hostId: 'local', repoId: 'same-repo' },
+        { hostId: 'runtime:env-1', repoId: 'same-repo' },
+        { hostId: 'local', repoId: 'bravo' },
+        { hostId: 'runtime:env-1', repoId: 'charlie' }
+      ]
+    })
+    expect(reposReorderForHost).toHaveBeenCalledWith({
+      hostId: 'local',
+      orderedIds: ['same-repo', 'bravo']
+    })
+    expect(runtimeEnvironmentCall).toHaveBeenCalledWith({
+      selector: 'env-1',
+      method: 'repo.reorder',
+      params: { orderedIds: ['same-repo', 'charlie'] },
+      timeoutMs: 15_000
+    })
+  })
+
   it('persists a complete cross-host overlay alongside host-local permutations', async () => {
     reposReorderForHost.mockResolvedValue({ status: 'applied' })
     runtimeEnvironmentCall.mockResolvedValue({