Really? I'll have to look into that if it's true. The game shouldn't require you to do that.
Still, I hope you enjoy the new update!
Edit: I looked into it and everything seems to be working fine. Are you sure you didn't save at a part of the story where the code was removed?
Because there's the part in the code where I talk with the player after the first act is done which was removed in this version. So if you saved there, then that might've broken your game.