diff --git a/pym/update/update.py b/pym/update/update.py
index 8c0e8a1..0f8a972 100644
--- a/pym/update/update.py
+++ b/pym/update/update.py
@@ -230,6 +230,8 @@ class Update(MethodsInterface):
                         status = git.getStatusInfo(rpath)
                         if not status or status['files']:
                             need_update = True
+                
+
                 except GitError as e:
                     need_update = True
                 if need_update:
@@ -431,8 +433,18 @@ class Update(MethodsInterface):
                                              cb_progress=self.setProgress,
                                              clean=check_status,
                                              notask=fallback_sync)
-                        removeDir(rpath)
-                        shutil.move(rpath_new, rpath)
+                        if not isinstance(e, NotGitError):
+                            removeDir(rpath)    
+                            shutil.move(rpath_new, rpath)
+                        else:
+                            #delete everything in rpath dir, but not rpath itself
+                            for root, dirs, files in os.walk(rpath):
+                                for f in files:
+                                    os.unlink(os.path.join(root, f))
+                                for d in dirs:
+                                    shutil.rmtree(os.path.join(root, d))
+                            for i in os.listdir(rpath_new):
+                                shutil.move(os.path.join(rpath_new, i), rpath)
                     except OSError as e:
                         raise UpdateError(_("Failed to modify the "
                                             "{repname} repository").format(