Sometimes I have luck interrogating Claude on why it did something. It'll either point to a skill or agent file with the culprit, or it'll respond with some vapid nonsense and apologize.
I ask because when I started informing it I made personal edits, it stopped doing this kind of thing so often and let me work _with_ it more.
My saved prompt now says never to assume a file has not been edited since the last time it was read between prompts.