diff --git a/flask_annex/file.py b/flask_annex/file.py
index 3d6d8ba..6ed8cf0 100644
--- a/flask_annex/file.py
+++ b/flask_annex/file.py
@@ -36,9 +36,10 @@ def _clean_empty_dirs(self, key):
             try:
                 os.rmdir(dir_name)
             except OSError as e:
-                if e.errno != errno.ENOTEMPTY:
+                if e.errno == errno.ENOTEMPTY:
+                    break
+                if e.errno != errno.ENOENT:
                     raise  # pragma: no cover
-                break
 
             key_dir_name = os.path.dirname(key_dir_name)
 
diff --git a/tests/helpers.py b/tests/helpers.py
index b2a66fe..9c90042 100644
--- a/tests/helpers.py
+++ b/tests/helpers.py
@@ -79,5 +79,5 @@ def test_delete_nonexistent(self, annex):
 
     def test_delete_many(self, annex):
         assert annex.list_keys('')
-        annex.delete_many(('foo/bar.txt', 'foo/baz.json', '@@nonexistent'))
+        annex.delete_many(('foo/bar.txt', 'foo/baz.json', 'foo/@@nonexistent'))
         assert not annex.list_keys('')