diff --git a/project.py b/project.py
index d887a558..9dc7feae 100644
--- a/project.py
+++ b/project.py
@@ -1277,7 +1277,20 @@ class Project:
         if is_new:
             self._InitGitDir(force_sync=force_sync, quiet=quiet)
         else:
-            self._UpdateHooks(quiet=quiet)
+            try:
+                # At this point, it's possible that gitdir points to an old
+                # objdir (e.g. name changed, but objdir exists). Check
+                # references to ensure that's not the case. See
+                # https://issues.gerritcodereview.com/40013418 for more
+                # details.
+                self._CheckDirReference(self.objdir, self.gitdir)
+
+                self._UpdateHooks(quiet=quiet)
+            except GitError as e:
+                if not force_sync:
+                    raise e
+                # Let _InitGitDir fix the issue, force_sync is always True here.
+                self._InitGitDir(force_sync=True, quiet=quiet)
         self._InitRemote()
 
         if self.UseAlternates: