Issue (bug?) with adding bookmarks and links

Recently I can no longer add links and bookmarks in a specific Scrivener document. If I add one, all pieces of text get the same link/bookmark and the same thing happens if I remove it again, then all links disappear. I find this quite disastrous. Is this a bug? How do I solve this? Restarting did nothing.
Bookmarking and adding links in other documents works well, it is only this one document that I use as a reference work and in which I collect everything that is important to cite sources in my books. So I have now lost everything I linked and bookmarked earlier, but I can’t solve it, because this ‘bug’ keeps bugging me.

Firstly, make sure you are up to date, with 3.1.5.1, as this sounds like an older bug.

That said, I’m not sure if all of the results of that older bug would be fixed by the newer version. So if it is still there, I would try using File ▸ Export ▸ Files... on this particular section, and use HTML as the export format. It should be easy to see from that, in a text editor, if the other links being obscured by this are really there are not, or at least be able to copy and paste the URLs back in.

At some level this may just be easiest to restore from a backup, as well, rather than trying to “repair”.

Thank you Amber, I updated, but that didn’t work. So I installed it again and transferred the files to a new document. That helped.

If you’re linking to external material using Add External Bookmark and you move the external material around, it will break the link in Scrivener. Mac users seem to overcome this by using aliases, but such doesn’t exist on Windows systems—a Windows dilemma, not a Scrivener responsibility.
If you’re linking internally, using Link to Document in Scrivener, and you move your material around, the link won’t break, unless, for example, you link to a character sheet called John and you decide to delete that character sheet and create a new one called John, then the link will no longer exist, because, invisible to you, John is really a document of some 16 numbers in Scrivener’s indexing, or whatever it’s called.