WIP: Cleanup orphan references when updating MR

What does this MR do?

Fixes https://gitlab.com/gitlab-org/gitlab-ce/issues/22014

Are there points in the code the reviewer needs to double check?

This MR is not finished yet, I will update this section after unwipping MR. Before sending the code to review I'm going to rewrite current fix a little bit, add tests and probably migration for existing orphaned references.

Why was this MR needed?

See https://gitlab.com/gitlab-org/gitlab-ce/issues/22014

Screenshots (if relevant)

Does this MR meet the acceptance criteria?

• CHANGELOG entry added
• Documentation created/updated
• API support added
• Tests
  • Added for this feature/bug
  • All builds are passing
• Conform by the merge request performance guides
• Conform by the style guides
• Branch has no merge conflicts with master (if you do - rebase it please)
• Squashed related commits together

What are the relevant issue numbers?

https://gitlab.com/gitlab-org/gitlab-ce/issues/22014