I have encountered the same problem. I do not know what causes it, but have found that directly copying the old repositories folder’s contents into the new one after performing the restore (including the db) solves the empty repo problem. You will have to fix permissions (chown -R git:git <repo folder> within container, or 998:998 from outside) and restart gitlab afterwards. I had to overwrite the existing +gitaly folder and .gitaly-metadata file, which was fine because there weren’t any projects in the new repos folder yet. I’m not sure about merging those files, I would back them up before overwriting in any case. Hope that helps. Feel free to shoot me a direct message if not.