Moved tracks?!

When I opened a a two and a half hour music video project yesterday after a break, I was shocked to find that the tracks that had been meticulously aligned had shifted. In the front part on V1 there is a gaping hole, on V2 I see smaller holes where there shouldn't be any. The audio tracks are also affected. The project is broken because I don't remember what I thought when I created the transitions. I've noticed this before, but I assumed that I must have done something wrong and overlooked it. But now I'm sure I wasn't the problem. It's just a private project that never gets published, but the time invested is enormous. I don't know how to handle it yet, should I report it as a bug and how should I prove it? Has anyone seen anything like it?