diff --git a/apps/server/src/storageCleanup.test.ts b/apps/server/src/storageCleanup.test.ts
index de1ccfefcf64f..3c1913439fa7f 100644
--- a/apps/server/src/storageCleanup.test.ts
+++ b/apps/server/src/storageCleanup.test.ts
@@ -2450,6 +2450,26 @@ describe("storage cleanup reports and local file policies", () => {
       }),
     ),
   );
+  it.live("keeps a thread's recreated worktree folder that has no .git", () =>
+    runCleanupTest(
+      Effect.gen(function* () {
+        const fixture = yield* cleanupFixture();
+        yield* fixture.command(fixture.repo, ["worktree", "remove", fixture.worktree]);
+        yield* fixture.fs.makeDirectory(`${fixture.worktree}/node_modules`, { recursive: true });
+        yield* fixture.fs.writeFileString(`${fixture.worktree}/yarn.lock`, "# lockfile\n");
+        expect((yield* fixture.service.runNow).entries).toEqual([
+          expect.objectContaining({
+            path: fixture.worktree,
+            outcome: "kept",
+            reason: "Not a linked worktree",
+          }),
+        ]);
+        expect(yield* fixture.fs.readFileString(`${fixture.worktree}/yarn.lock`)).toBe(
+          "# lockfile\n",
+        );
+      }),
+    ),
+  );
   it.live.each([
     ["any-local-files", ".env", "kept"],
     ["uncommitted-changes", ".env", "removed"],
diff --git a/apps/server/src/storageCleanup.ts b/apps/server/src/storageCleanup.ts
index a5f9cd7eefa12..a4e6064910f79 100644
--- a/apps/server/src/storageCleanup.ts
+++ b/apps/server/src/storageCleanup.ts
@@ -846,7 +846,8 @@ const make = Effect.gen(function* () {
         return "worktree is a symbolic link";
       if (!roots.some((root) => inside(root, realPath)))
         return "outside the managed worktree folder";
-      if ((yield* fs.stat(path.join(worktreePath, ".git"))).type !== "File")
+      const gitPath = path.join(worktreePath, ".git");
+      if (!(yield* fs.exists(gitPath)) || (yield* fs.stat(gitPath)).type !== "File")
         return "not a linked worktree";
       return null;
     });