diff --git a/src/main/persistence.test.ts b/src/main/persistence.test.ts
index c7f255dafb4..419016f6f83 100644
--- a/src/main/persistence.test.ts
+++ b/src/main/persistence.test.ts
@@ -4634,6 +4634,42 @@ describe('Store', () => {
     expect(store.getWorktreeLineage(deadKey)).toBeUndefined()
   })
 
+  it('never GCs folder-workspace instance metas — the meta IS the workspace', async () => {
+    const OLD = Date.now() - 40 * 24 * 60 * 60 * 1000
+    const folderInstanceKey = `r1::${join(testState.dir, 'gone-folder')}::workspace:11111111-1111-4111-8111-111111111111`
+    writeDataFile({
+      repos: [makeRepo({ kind: 'folder' })],
+      worktreeMeta: {
+        [folderInstanceKey]: { displayName: 'Session A', comment: '', lastActivityAt: OLD }
+      }
+    })
+
+    const store = await createStore()
+    expect(Object.keys(store.getAllWorktreeMeta())).toContain(folderInstanceKey)
+  })
+
+  it('never GCs Linux-style WSL worktree paths on Windows', async () => {
+    const OLD = Date.now() - 40 * 24 * 60 * 60 * 1000
+    const wslLinkedKey = 'r1::/home/user/gone-worktree'
+    writeDataFile({
+      repos: [makeRepo()],
+      worktreeMeta: {
+        [wslLinkedKey]: { displayName: '', comment: '', lastActivityAt: OLD }
+      }
+    })
+
+    await withPlatform('win32', async () => {
+      const store = await createStore()
+      expect(Object.keys(store.getAllWorktreeMeta())).toContain(wslLinkedKey)
+    })
+  })
+
+  it('tolerates a null worktreeMeta map in the durable file', async () => {
+    writeDataFile({ worktreeMeta: null })
+    const store = await createStore()
+    expect(store.getAllWorktreeMeta()).toEqual({})
+  })
+
   // ── GitHub cache sidecar ───────────────────────────────────────────
 
   it('cache refreshes never rewrite the durable state file', async () => {
diff --git a/src/main/persistence.ts b/src/main/persistence.ts
index 1fe9193bf1d..14f3da845bc 100644
--- a/src/main/persistence.ts
+++ b/src/main/persistence.ts
@@ -126,9 +126,14 @@ import {
 import { agentHookServer } from './agent-hooks/server'
 import { pruneLocalTerminalScrollbackBuffers } from '../shared/workspace-session-terminal-buffers'
 import { pruneWorkspaceSessionBrowserHistory } from '../shared/workspace-session-browser-history'
-import { getRepoIdFromWorktreeId, getWorktreePathBasenameFromId } from '../shared/worktree-id'
+import {
+  FOLDER_WORKSPACE_INSTANCE_SEPARATOR,
+  getRepoIdFromWorktreeId,
+  getWorktreePathBasenameFromId
+} from '../shared/worktree-id'
 import {
   isPathInsideOrEqual,
+  isWindowsAbsolutePathLike,
   normalizeRuntimePathForComparison
 } from '../shared/cross-platform-path'
 import { normalizeTerminalQuickCommands } from '../shared/terminal-quick-commands'
@@ -347,11 +352,20 @@ function getGithubCacheFile(): string {
 const WORKTREE_META_GC_GRACE_MS = 30 * 24 * 60 * 60 * 1000
 
 function gcStaleWorktreeMeta(state: PersistedState): number {
+  // Why: a hand-corrupted file with `"worktreeMeta": null` overrides the
+  // defaults merge; normalize instead of throwing outside the parse guard.
+  state.worktreeMeta ??= {}
   const repoById = new Map(state.repos.map((repo) => [repo.id, repo]))
   const projectIds = new Set((state.projects ?? []).map((project) => project.id))
   const now = Date.now()
   let removed = 0
   for (const key of Object.keys(state.worktreeMeta)) {
+    // Why: folder-project workspace instances are keyed
+    // `repoId::path::workspace:<uuid>` and their meta IS the workspace
+    // record — never a filesystem-checkout row. Skip them entirely.
+    if (key.includes(FOLDER_WORKSPACE_INSTANCE_SEPARATOR)) {
+      continue
+    }
     const separator = key.indexOf('::')
     if (separator === -1) {
       continue
@@ -377,16 +391,24 @@ function gcStaleWorktreeMeta(state: PersistedState): number {
     if (!isAbsolute(worktreePath) || isWslUncPath(worktreePath)) {
       continue
     }
-    if (existsSync(worktreePath)) {
+    // Why: WSL linked worktrees on Windows carry Linux-style paths from git
+    // porcelain; a Windows existsSync cannot probe those and would falsely
+    // condemn live worktrees.
+    if (process.platform === 'win32' && !isWindowsAbsolutePathLike(worktreePath)) {
       continue
     }
     // Why keep timestamp-less entries: without lastActivityAt/createdAt we
     // cannot prove the 30-day idle grace elapsed; the measured dead entries
     // all carry timestamps, so this costs almost nothing in reclaimed bytes.
+    // Grace runs before the stat so healthy profiles skip the existsSync
+    // fan-out (and its slow-NFS tail) for active entries entirely.
     const newestTouch = Math.max(meta?.lastActivityAt ?? 0, meta?.createdAt ?? 0)
     if (newestTouch === 0 || now - newestTouch < WORKTREE_META_GC_GRACE_MS) {
       continue
     }
+    if (existsSync(worktreePath)) {
+      continue
+    }
     delete state.worktreeMeta[key]
     delete state.worktreeLineageById[key]
     delete state.workspaceLineageByChildKey[worktreeWorkspaceKey(key)]