Repository empty when fileserver went away for 2 days

My local GitLab server is using a remote fileserver for storing al repositories. However, after having issues with the fileserver, I took it offline for 2 days. Now sinds that period of time all backups created by GitLab are just less then 1 MB, and all repo’s in the UI are marked as empty.

The fileserver is now properly mounted and reachable again, however I cannot get GitLab to re-initialize the repositories again. How can I fix this?