Our organization has been using links in commit comments (on Github) to cross-reference to issues, taking advantage of the automated feature that puts links back to all the relevant commits on the issue page.
Recently, some cross-references were added to several commits by mistake. The erroneous commit comments have been deleted, but the cross-references from the issues back to the commits are still showing on the issue pages. It has been two weeks, and it has not refreshed.
Is there anything we can do about this?
git is designed in such a way to do its best to avoid losing information. One of the ways that it achieves this is that it is a "write-only" system. This means that you can write new information to the git repository but once written, you can't edit it. You can delete it. You can create something that looks a lot like it with some details changed. But you can't edit a record, including a commit.
So when you amend a commit to change its commit message, you're creating a new commit with the same contents except a different commit message. What this means in your case is that the old commit that originally linked to the issue is still there, only orphaned.
If you want to permanently delete the commit from your GitHub repository, you can contact private support to help with that at https://github.com/contact. I'm not sure if they'll be able to remove the reference, but private support will be able to tell you more about your options.
I hope that helps.