Did this update fix you ignoring the bots in factory 2 and getting locked out of the rest of the story? If not it's insane that you'd make people restart the whole game for one simple choice.
I have 30k hearts I doubt that's the issue. I'm unable to gain entry to the church because I ingored the bots and nothing I've found or done has fixed this. I won't try this new update if I'm forced to replay hours of story to fix this.