I added the Act Select to alleviate this problem. If you're on Act 6, you can just start the act from Act Select and choose which path you're on.
The game is still in development and a lot changes every update. So the saves will always be questionable. Remember, this is my first game so I'm still learning. And as I learn, I go back and improve old code. That leads to problems with saves.
I truly am sorry but I worked really hard on the Act Select specifically because of this problem. I hope it's sufficient.