Premiere Pro project was fine but on second open suddenly messed up and out of sync

Hello! In my 10 years of video editing experience I have never come across this error/bug/problem.

So I've finished my project, rendered and exported video. Closed it.

After the client wants me to adjust some minor changes, I open up my project and suddenly everything is mixed up, out of sync, a total mess, cuts on the timeline are the same, but references to where the cuts are in the original clips are complete random and not where I've cut them on the original session.

Raw footage didn't change, is there any possible solution to this? I mean, thank god I have my renders and can work the changes on top of them, even tho it's not the best option, but I lost 5 hours of editing to this bug/error and don't know how to fix it. 

Thanks for any tips on this if anyone knows.