According to the error message there is an unreachable object in the database, maybe a result of an upstream force-push. The error should be cleaned up automatically after a while, due to Gitlab's automatic housekeeping. If you don't want to wait that long, you can run the housekeeping task manually on the faulty repositories:
First identify the Gitaly relative path for the faulty repository:
Web UI: In the admin area go to Overview → Projects and select the project in question. The path is displayed in the field "Gitaly relative path" in the "Project info" box.
Command line: Start a Rails console as root (this may take a long time, so be patient).
After the prompt appears enter one of the following commands:
Project.find(42).disk_path # find by project ID
Project.find_by_full_path('GROUP_NAME/PROJECT_NAME').disk_path # find by project name
Alternatively you can use the
runner subcommand for non-interactive execution. In that case you need to prefix the command with
pp ("pretty-print") to actually display the returned value.
gitlab-rails runner "puts Project.find(42).disk_path"
Once you have determined the Gitaly path log into your Gitlab server (if you haven't already) and run the following command as root:
/opt/gitlab/embedded/bin/git -C /var/opt/gitlab/git-data/repositories/@hashed/c0/ff/eed0...0d.git
Replace the example relative path (
@hashed/c0/ff/eed0...0d.git) with your actual relative path.