Restoring a GitLab instance using Docker Swarm can sometimes result in the Git repositories not being restored properly, even if the database and other components are successfully restored.

It looks like the issue is that the Git repositories aren't being restored properly when you're using the GitLab backup/restore process. Here are some steps you can follow to troubleshoot and fix this:

1. Check the Backup File: Make sure the backup file (<backup-id>_gitlab_backup.tar) actually includes the repository data. You can extract or list the contents of the backup file to confirm.

2. Verify Docker Volumes: If you're using Docker, ensure the volume for repository data (usually /var/opt/gitlab) is mounted correctly. If the data wasn't backed up properly due to misconfigured volumes, it won't restore.

3. Use the Correct Restore Command: When restoring, you need to specify the backup ID correctly. For example:

docker exec -t <container_name> gitlab-backup restore BACKUP=<backup-id>

Replace <container_name> with your container's name and <backup-id> with the correct ID of your backup.

4. Match GitLab Versions: The version of GitLab you're restoring to must match the version from which the backup was created. Mismatched versions can lead to issues during the restore process.

5. Monitor for Errors: During the restore process, check the logs for any errors or warnings. These often point to what went wrong.

6. Review Configuration: Make sure your GitLab configuration (like repository paths in /etc/gitlab/gitlab.rb) is set up properly. Incorrect settings here could cause the restore process to skip the repositories.

7. Check Permissions: If the files are restored but GitLab can't access them, it might be a permissions issue. Ensure the correct ownership and permissions are applied to the restored data.

If you've gone through these steps and it still doesn't work, feel free to share more details. For example, any specific error messages or your setup (like Docker Swarm or standalone installation). It might help narrow down the issue!