diff --git a/gclient_scm.py b/gclient_scm.py
index ab07b830d..e0a90912e 100644
--- a/gclient_scm.py
+++ b/gclient_scm.py
@@ -353,7 +353,10 @@ class GitWrapper(SCMWrapper):
          not os.path.exists(os.path.join(self.checkout_path, '.git')))):
       if (os.path.isdir(self.checkout_path) and
           not os.path.exists(os.path.join(self.checkout_path, '.git'))):
-        self._DeleteOrMove(options.force)
+        # This is a little hack to work around checkouts which are created
+        # using "gclient config --name ."
+        if not self.relpath == '.':
+          self._DeleteOrMove(options.force)
       self._Clone(revision, url, options)
       self._UpdateBranchHeads(options, fetch=True)
       if file_list is not None: