diff --git a/src/python/OBis/obis/dm/data_mgmt.py b/src/python/OBis/obis/dm/data_mgmt.py
index 6899cbf6718d2771053a955e4a2aa4251917435e..a156969f84781443f959fb0fb8a34a49a9c7fa73 100644
--- a/src/python/OBis/obis/dm/data_mgmt.py
+++ b/src/python/OBis/obis/dm/data_mgmt.py
@@ -311,6 +311,7 @@ class GitDataMgmt(AbstractDataMgmt):
         self.git_wrapper.git_reset_to(self.previous_git_commit_hash)
         properties_path = self.config_resolver.local_public_properties_path()
         self.git_wrapper.git_checkout(properties_path)
+        self.git_wrapper.git_delete_if_untracked('.obis/properties.json')
 
     def clone(self, data_set_id, ssh_user, content_copy_index):
         try:
diff --git a/src/python/OBis/obis/dm/git.py b/src/python/OBis/obis/dm/git.py
index cdfea134597969b313553558271f58c6ed70a021..656f17af1ef16da58c94176bfbfd17ad562dc22e 100644
--- a/src/python/OBis/obis/dm/git.py
+++ b/src/python/OBis/obis/dm/git.py
@@ -86,6 +86,10 @@ class GitWrapper(object):
                 gitignore.write(path)
                 gitignore.write("\n")
 
+    def git_delete_if_untracked(self, file):
+        result = run_shell([self.git_path, 'ls-files', '--error-unmatch', file])
+        if file in result.output:
+            run_shell(['rm', file])
 
 class GitRepoFileInfo(object):
     """Class that gathers checksums and file lengths for all files in the repo."""