diff --git a/apps/server/src/vcs/GitVcsDriver.test.ts b/apps/server/src/vcs/GitVcsDriver.test.ts
index a6bbef6ed1de09e0efaf1488484b22f7dec8df42..3a7a16f95d4cca32c5159dba3c1dc17f8a3d33d2 100644
--- a/apps/server/src/vcs/GitVcsDriver.test.ts
+++ b/apps/server/src/vcs/GitVcsDriver.test.ts
@@ -1049,6 +1049,7 @@ it.effect("restores empty checkpoints without changing paths outside the workspa
             fallbackToHead: false,
           }),
         );
+        assert.isTrue(yield* fileSystem.exists(cwd));
         assert.isFalse(yield* fileSystem.exists(addedPath));
       }
       yield* fileSystem.writeFileString(
diff --git a/apps/server/src/vcs/GitVcsDriver.ts b/apps/server/src/vcs/GitVcsDriver.ts
index 599269791edf1a11dbfc2cdfdd10a6b0033050ec..3803c78fc6d2e61e8bf0ce2eede04ee342493acf 100644
--- a/apps/server/src/vcs/GitVcsDriver.ts
+++ b/apps/server/src/vcs/GitVcsDriver.ts
@@ -1114,7 +1114,7 @@ export const makeVcsDriverShape = Effect.fn("makeGitVcsDriverShape")(function* (
         });
       }
       // Restoring away the last tracked file can remove a nested workspace directory.
-      yield* fileSystem.makeDirectory(input.cwd, { recursive: true }).pipe(
+      const recreateWorkspace = fileSystem.makeDirectory(input.cwd, { recursive: true }).pipe(
         Effect.mapError(
           (cause) =>
             new VcsProcessExitError({
@@ -1126,6 +1126,7 @@ export const makeVcsDriverShape = Effect.fn("makeGitVcsDriverShape")(function* (
             }),
         ),
       );
+      yield* recreateWorkspace;
       const cleaned = yield* execute({
         operation,
         cwd: input.cwd,
@@ -1150,6 +1151,8 @@ export const makeVcsDriverShape = Effect.fn("makeGitVcsDriverShape")(function* (
             detail: cleaned.stderr.trim() || "Could not clean the checkpoint workspace.",
           });
       }
+      // On Windows the same clean can remove './' and exit 0.
+      yield* recreateWorkspace;
 
       const headExists = yield* hasHeadCommit(input.cwd);
       if (headExists) {