Ok, I get it, that was actually a great way you put it. I made it so restarting works always, which is why I couldn't replicate this bug, but if you continue instead, the flags don't get reset after all. You solved this mystery!
Viewing post in Aftershift: the Post-TF game comments
I didn't expect to have any audience from itch so the actual bug reporting was meant to be handled on FA. There is an option to make threads under the game, but it removes all comments and I can't make said threads until after I save this change... it seems poorly designed. Unless you mean making a bug post in the same way devlogs are made, though I didn't find a way to order them or make them sticky.