diff --git a/rhodecode/controllers/admin/settings.py b/rhodecode/controllers/admin/settings.py
--- a/rhodecode/controllers/admin/settings.py
+++ b/rhodecode/controllers/admin/settings.py
@@ -113,16 +113,16 @@ class SettingsController(BaseController)
         if setting_id == 'mapping':
             rm_obsolete = request.POST.get('destroy', False)
             invalidate_cache = request.POST.get('invalidate', False)
-            log.debug('rescanning directories with destroy obsolete=%s'
+            log.debug('rescanning repo location with destroy obsolete=%s'
                       % (rm_obsolete,))
-            initial = ScmModel().repo_scan()
 
             if invalidate_cache:
                 log.debug('invalidating all repositories cache')
-                for repo_name in initial.keys():
-                    ScmModel().mark_for_invalidation(repo_name)
+                for repo in Repository.get_all():
+                    ScmModel().mark_for_invalidation(repo.repo_name)
 
-            added, removed = repo2db_mapper(initial, rm_obsolete)
+            filesystem_repos = ScmModel().repo_scan()
+            added, removed = repo2db_mapper(filesystem_repos, rm_obsolete)
             _repr = lambda l: ', '.join(map(safe_unicode, l)) or '-'
             h.flash(_('Repositories successfully '
                       'rescanned added: %s ; removed: %s') %