diff --git a/gclient.py b/gclient.py
index f71eccc4c3..5b159edb04 100755
--- a/gclient.py
+++ b/gclient.py
@@ -1134,6 +1134,9 @@ solutions = [
       # Only delete the directory if there are no changes in it, and
       # delete_unversioned_trees is set to true.
       entries = [i.name for i in self.root.subtree(False) if i.url]
+      full_entries = [os.path.join(self.root_dir, e.replace('/', os.path.sep))
+                      for e in entries]
+
       for entry, prev_url in self._ReadEntries().iteritems():
         if not prev_url:
           # entry must have been overridden via .gclient custom_deps
@@ -1152,8 +1155,15 @@ solutions = [
         if (entry not in entries and
             (not any(path.startswith(entry + '/') for path in entries)) and
             os.path.exists(e_dir)):
-          file_list = []
           scm = gclient_scm.CreateSCM(prev_url, self.root_dir, entry_fixed)
+
+          # Check to see if this directory is now part of a higher-up checkout.
+          if scm.GetCheckoutRoot() in full_entries:
+            logging.info('%s is part of a higher level checkout, not '
+                         'removing.', scm.GetCheckoutRoot())
+            continue
+
+          file_list = []
           scm.status(self._options, [], file_list)
           modified_files = file_list != []
           if (not self._options.delete_unversioned_trees or
diff --git a/gclient_scm.py b/gclient_scm.py
index ba49f050c6..01dfd54675 100644
--- a/gclient_scm.py
+++ b/gclient_scm.py
@@ -173,6 +173,9 @@ class GitWrapper(SCMWrapper):
     except OSError:
       return False
 
+  def GetCheckoutRoot(self):
+    return scm.GIT.GetCheckoutRoot(self.checkout_path)
+
   def GetRevisionDate(self, revision):
     """Returns the given revision's date in ISO-8601 format (which contains the
     time zone)."""
@@ -920,6 +923,9 @@ class SVNWrapper(SCMWrapper):
     except OSError:
       return False
 
+  def GetCheckoutRoot(self):
+    return scm.SVN.GetCheckoutRoot(self.checkout_path)
+
   def GetRevisionDate(self, revision):
     """Returns the given revision's date in ISO-8601 format (which contains the
     time zone)."""
diff --git a/tests/gclient_scm_test.py b/tests/gclient_scm_test.py
index 5f5af69b6c..6cc7927d2f 100755
--- a/tests/gclient_scm_test.py
+++ b/tests/gclient_scm_test.py
@@ -102,6 +102,7 @@ class SVNWrapperTestCase(BaseTestCase):
     members = [
         'BinaryExists',
         'FullUrlForRelativeUrl',
+        'GetCheckoutRoot',
         'GetRevisionDate',
         'GetUsableRev',
         'RunCommand',
@@ -789,6 +790,7 @@ class ManagedGitWrapperTestCase(BaseGitWrapperTestCase):
     members = [
         'BinaryExists',
         'FullUrlForRelativeUrl',
+        'GetCheckoutRoot',
         'GetRevisionDate',
         'GetUsableRev',
         'RunCommand',