diff --git a/src/main/runtime/workspaces/catalog/repo-worktree-row-resolution.test.ts b/src/main/runtime/workspaces/catalog/repo-worktree-row-resolution.test.ts
index 0716d24874e..7418e2203ed 100644
--- a/src/main/runtime/workspaces/catalog/repo-worktree-row-resolution.test.ts
+++ b/src/main/runtime/workspaces/catalog/repo-worktree-row-resolution.test.ts
@@ -1,6 +1,7 @@
 import { describe, expect, it, vi } from 'vitest'
 
 import type { Repo } from '../../../../shared/repo-types'
+import type { WorktreeLineage } from '../../../../shared/worktree/lineage-types'
 import type { WorktreeMeta } from '../../../../shared/worktree/meta-types'
 
 import type { GitWorktreeInfo, Worktree } from '../../../../shared/worktree/types'
@@ -10,9 +11,11 @@ import { buildDetectedGitWorktrees } from '../../../ipc/worktrees/listing/ssh-wo
 import {
   resolveRepoWorktreeRows,
   resolveScopedWorktreeIdRow,
+  scanRepoWorktreeRows,
   type RepoWorktreeRowDeps
 } from './repo-worktree-row-resolution'
 import type { HostWorktreeTarget } from '../../../../shared/worktree/host-qualified-identity'
+import { bumpLocalWorktreeScanGeneration } from '../../../workspaces/catalog/local-worktree-scan-generation'
 
 function repo(
   id: string,
@@ -160,6 +163,39 @@ describe('scoped worktree id resolution across path spellings (#16243)', () => {
   })
 })
 
+describe('scanRepoWorktreeRows lineage pruning', () => {
+  // #16654: lineage written by a create that overtook the scan must survive its stale rows.
+  it('keeps lineage recorded by a worktree change that overtook the scan', async () => {
+    const owner = repo('repo-1', '/repo')
+    const deps = createDeps([owner])
+    const childId = 'repo-1::/repo-child'
+    const lineageById: Record<string, WorktreeLineage> = {}
+    const removeWorktreeLineage = vi.fn()
+    Object.assign(deps.store, {
+      getAllWorktreeLineage: () => lineageById,
+      getWorktreeMeta: () => undefined,
+      removeWorktreeLineage
+    })
+    deps.scanRepo.mockImplementationOnce(async () => {
+      bumpLocalWorktreeScanGeneration(owner.id)
+      lineageById[childId] = {
+        worktreeId: childId,
+        worktreeInstanceId: 'child-instance',
+        parentWorktreeId: 'repo-1::/repo',
+        parentWorktreeInstanceId: 'parent-instance',
+        origin: 'cli',
+        capture: { source: 'explicit-cli-flag', confidence: 'explicit' },
+        createdAt: 1
+      }
+      return { ok: true, worktrees: [gitWorktree('/repo')] }
+    })
+
+    await scanRepoWorktreeRows(deps, owner, new Map())
+
+    expect(removeWorktreeLineage).not.toHaveBeenCalled()
+  })
+})
+
 describe('folder-to-Git checkout identity', () => {
   it.each([
     ['C:\\projects\\draft', 'C:/projects/draft'],
diff --git a/src/main/runtime/workspaces/catalog/repo-worktree-row-resolution.ts b/src/main/runtime/workspaces/catalog/repo-worktree-row-resolution.ts
index 980b21d816c..637892c7758 100644
--- a/src/main/runtime/workspaces/catalog/repo-worktree-row-resolution.ts
+++ b/src/main/runtime/workspaces/catalog/repo-worktree-row-resolution.ts
@@ -28,6 +28,7 @@ import { createRepoRowExecutionHostLookup } from '../../../../shared/execution-h
 import { areWorktreePathsEqual } from '../../../git/worktrees/catalog/worktree-path-comparison'
 import { mergeWorktree } from '../../../ipc/worktree-metadata-merge'
 import { pruneLineageForMissingRepoWorktrees } from '../../../workspaces/catalog/worktree-lineage-pruning'
+import { getLocalWorktreeScanGeneration } from '../../../workspaces/catalog/local-worktree-scan-generation'
 import { getRepoOwnedWorktreeMeta } from '../../../workspaces/catalog/worktree-metadata-ownership'
 import { resolveLocalProjectRuntimesForRepos } from '../../../workspaces/execution-host/local-project-runtime-resolution'
 import type { RuntimeWorktreeScanResult } from './repo-worktree-resolution-scan'
@@ -117,6 +118,7 @@ export async function scanRepoWorktreeRows(
   repoOwnerCount = deps.store.getRepos().filter((candidate) => candidate.id === repo.id).length
 ): Promise<RepoWorktreeRowsScan> {
   const { store } = deps
+  const scanGeneration = getLocalWorktreeScanGeneration(repo.id)
   // Absorb rejection before withTimeout: rejection preserves shipped empty results, but timeout restores last-known rows.
   const scan: RuntimeWorktreeScanResult = (await withTimeout<RuntimeWorktreeScanResult | null>(
     deps
@@ -132,7 +134,7 @@ export async function scanRepoWorktreeRows(
   }
   const gitWorktrees = preserveFolderUpgradeWorktreePath(repo, scan.worktrees)
   if (scan.ok) {
-    pruneLineageForMissingRepoWorktrees(store, repo, gitWorktrees)
+    pruneLineageForMissingRepoWorktrees(store, repo, gitWorktrees, { scanGeneration })
   }
   return { ok: scan.ok, worktrees: gitWorktrees }
 }
diff --git a/src/main/runtime/workspaces/catalog/runtime-managed-worktree-queries.test.ts b/src/main/runtime/workspaces/catalog/runtime-managed-worktree-queries.test.ts
index 601576ebea6..464deed5b46 100644
--- a/src/main/runtime/workspaces/catalog/runtime-managed-worktree-queries.test.ts
+++ b/src/main/runtime/workspaces/catalog/runtime-managed-worktree-queries.test.ts
@@ -38,6 +38,7 @@ import { RuntimeManagedWorktreeQueries } from './runtime-managed-worktree-querie
 import type { RuntimeStore } from '../../construction/runtime-store-contract'
 import {
   bumpLocalWorktreeScanGeneration,
+  getLocalWorktreeScanGeneration,
   resetLocalWorktreeScanGenerationsForTests
 } from '../../../workspaces/catalog/local-worktree-scan-generation'
 
@@ -287,6 +288,28 @@ describe('RuntimeManagedWorktreeQueries.listDetected overtaken scan', () => {
     expect(pruneLineageMock.mock.calls[0]?.[2]).toEqual(rows([repo.path, created]))
   })
 
+  // #16654: a create landing during the metadata probe writes lineage the scan never saw.
+  it('gates lineage pruning on the scan-start generation when a change lands during metadata pruning', async () => {
+    const store = gitStore({
+      pruneSessionlessMissingLocalWorktreeMetadataForRepo: vi.fn(() => []),
+      getProfileStorageDirectory: () => '/profile',
+      captureNativeLocalWorktreeMetadataScanExpectation: vi.fn(() => ({ repo, metadata: [] }))
+    })
+    const atScanStart = getLocalWorktreeScanGeneration(repo.id)
+    pruneMetadataMock.mockImplementationOnce(async () => {
+      bumpLocalWorktreeScanGeneration(repo.id)
+      return { scanGenerationCurrent: false, preservedMetadataCandidateIds: new Set() }
+    })
+    const scanRepo = vi.fn(async () => ({ ok: true as const, worktrees: rows([repo.path]) }))
+
+    await queries(store, { scanRepo }).listDetected(repo)
+
+    // The prune refuses a generation that has moved on; it must see the scan-start one.
+    expect(pruneLineageMock).toHaveBeenCalledWith(store, repo, rows([repo.path]), {
+      scanGeneration: atScanStart
+    })
+  })
+
   it('publishes the last scan non-authoritatively once the re-scan bound is spent', async () => {
     const scanRepo = vi.fn(overtakenScan([repo.path]))
 
diff --git a/src/main/runtime/workspaces/catalog/runtime-managed-worktree-queries.ts b/src/main/runtime/workspaces/catalog/runtime-managed-worktree-queries.ts
index 5d0c79c73b9..ed08471a010 100644
--- a/src/main/runtime/workspaces/catalog/runtime-managed-worktree-queries.ts
+++ b/src/main/runtime/workspaces/catalog/runtime-managed-worktree-queries.ts
@@ -173,7 +173,9 @@ export class RuntimeManagedWorktreeQueries {
           scanGeneration: scan.scanGeneration
         })
       }
-      pruneLineageForMissingRepoWorktrees(store, repo, scan.worktrees)
+      pruneLineageForMissingRepoWorktrees(store, repo, scan.worktrees, {
+        scanGeneration: scan.scanGeneration
+      })
     }
     const matcher = createWorktreeVisibilitySourceMatcher(
       [repo.path, ...scan.worktrees.map((worktree) => worktree.path)],
diff --git a/src/main/workspaces/catalog/worktree-lineage-pruning.ts b/src/main/workspaces/catalog/worktree-lineage-pruning.ts
index 001c6e6b80b..9a701ff5def 100644
--- a/src/main/workspaces/catalog/worktree-lineage-pruning.ts
+++ b/src/main/workspaces/catalog/worktree-lineage-pruning.ts
@@ -9,6 +9,7 @@ import { worktreeRetentionPathComparisonKey } from './worktree-retention-path-co
 import type { Store } from '../../persistence/loading-store/store'
 import { isWslMoveRepoBlocked } from '../../persistence/moving-wsl-projects/orchestration/wsl-move-background-backoff'
 import { hostWorktreeTarget } from '../../../shared/worktree/host-qualified-identity'
+import { isLocalWorktreeScanGenerationCurrent } from './local-worktree-scan-generation'
 
 type WorktreeLineagePruningStore = Pick<Store, 'getRepos' | 'getWorktreeMeta' | 'setWorktreeMeta'> &
   Partial<
@@ -58,12 +59,16 @@ export function pruneLineageForMissingRepoWorktrees(
   options: {
     platform?: NodeJS.Platform
     preservedMetadataCandidateIds?: ReadonlySet<string>
+    /** Scan-start generation; a worktree change since then may have recorded lineage these rows miss (#16654). */
+    scanGeneration?: number
   } = {}
 ): void {
-  const { platform = process.platform, preservedMetadataCandidateIds } = options
+  const { platform = process.platform, preservedMetadataCandidateIds, scanGeneration } = options
   // Mid-move a scan can miss paths that still exist; lineage waits for the move to settle.
   if (
     isWslMoveRepoBlocked(repo) ||
+    (scanGeneration !== undefined &&
+      !isLocalWorktreeScanGenerationCurrent(repo.id, scanGeneration)) ||
     typeof store.getAllWorktreeLineage !== 'function' ||
     typeof store.removeWorktreeLineage !== 'function'
   ) {