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 shouldnt be any. The audio tracks are also affected. The project is broken because I dont remember what I thought when I created the transitions. Ive noticed this before, but I assumed that I must have done something wrong and overlooked it. But now Im sure I wasnt the problem. Its just a private project that never gets published, but the time invested is enormous. I dont 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?