Hi,
thanks, we are one step further with a new error message to search for 
I found error: Could not read from object database for commit-graph (#2359) 路 Issues 路 GitLab.org / gitaly 路 GitLab which discusses the error message and potential workarounds, in GitLab projects failed their last repository check - #3 by DrrMrr
Before continuing, I鈥檇 suggest taking a backup of the git repository storage. It is a bit like operating on the open heart, although with git commands and no direct file handle manipulation. It would be bad if something breaks the repository and there鈥檚 no backup to rolback.
Can you try to run fsck, gc, fsck to see if that helps? Commands for easier copy-paste:
sudo -u git /opt/gitlab/embedded/bin/git -C /var/opt/gitlab/git-data/repositories/@hashed/96/06/96061e92f58e4bdcdee73df36183fe3ac64747c81c26f6c83aada8d2aabb1864.git fsck
sudo -u git /opt/gitlab/embedded/bin/git -C /var/opt/gitlab/git-data/repositories/@hashed/96/06/96061e92f58e4bdcdee73df36183fe3ac64747c81c26f6c83aada8d2aabb1864.git gc
sudo -u git /opt/gitlab/embedded/bin/git -C /var/opt/gitlab/git-data/repositories/@hashed/96/06/96061e92f58e4bdcdee73df36183fe3ac64747c81c26f6c83aada8d2aabb1864.git fsck
error: Could not read from object database for commit-graph (#2359) 路 Issues 路 GitLab.org / gitaly 路 GitLab has more suggestions for the commit graph fixes itself.
sudo -u git /opt/gitlab/embedded/bin/git -C /var/opt/gitlab/git-data/repositories/@hashed/96/06/96061e92f58e4bdcdee73df36183fe3ac64747c81c26f6c83aada8d2aabb1864.git fsck --lost-found
sudo -u git /opt/gitlab/embedded/bin/git -C /var/opt/gitlab/git-data/repositories/@hashed/96/06/96061e92f58e4bdcdee73df36183fe3ac64747c81c26f6c83aada8d2aabb1864.git commit-graph write
sudo -u git /opt/gitlab/embedded/bin/git -C /var/opt/gitlab/git-data/repositories/@hashed/96/06/96061e92f58e4bdcdee73df36183fe3ac64747c81c26f6c83aada8d2aabb1864.git reflog expire --expire=now --all
sudo -u git /opt/gitlab/embedded/bin/git -C /var/opt/gitlab/git-data/repositories/@hashed/96/06/96061e92f58e4bdcdee73df36183fe3ac64747c81c26f6c83aada8d2aabb1864.git gc --prune=now
And a last comment with new workarounds to try. error: Could not read from object database for commit-graph (#2359) 路 Issues 路 GitLab.org / gitaly 路 GitLab
I鈥檇 appreciate if you can test and report back whether it fixes your problems. I鈥檒l link this forum topic in the issue, feel free to comment there as well
Cheers,
Michae l