diff --git a/fdroidserver/deploy.py b/fdroidserver/deploy.py
index d514e569..dd856c96 100644
--- a/fdroidserver/deploy.py
+++ b/fdroidserver/deploy.py
@@ -511,13 +511,15 @@ def update_servergitmirrors(servergitmirrors, repo_section):
         enabled_remotes = []
         for d in servergitmirrors:
             index_only = d.get('index_only', False)
+
+            # Use a separate branch for the index only mode as it needs a different set of files to commit
             if index_only:
-                # Use a separate branch for the index only mode as it needs a different set of files to commit
-                repo.create_head('index_only', initial_branch_ref)
-                repo.heads.index_only.checkout()
+                branch_name = 'index_only'
             else:
-                repo.create_head('full', initial_branch_ref)
-                repo.heads.full.checkout()
+                branch_name = 'full'
+            if not branch_name in repo.heads:
+                repo.create_head(branch_name, initial_branch_ref)
+            repo.heads[branch_name].checkout()
 
             remote_url = d['url']
             name = REMOTE_HOSTNAME_REGEX.sub(r'\1', remote_url)