Upgrade gitlab leave .pack files?

We are deleting and optimizing the disk of our GitLab instance.

We have come across these files and we are not quite sure what they are. It may be that updating left these orphaned files.

Is it safe to delete them? What is the best option to do cleanup in Gitlab?

This isn’t unique to Gitlab, you should however be using git gc for such maintenance rather than thinking about deleting them manually: Git - Packfiles

This post should also help you: Repocheck dangling commit - #6 by dnsmichi