Thank you for telling me about this!
I believe just exiting the room should work, since you can still walk around when its dark(hell, thats part of the speedrun strat for skipping the mansion)
As for the second one, I'm going to hotfix that sometime tonight or in the morning, BUT I know as a failsafe, talking to knuckles in that area will reset any wacky modifiers put on the player.
(and for the third one, that'll also be fixed too. Right now I'm focusing on remaking AG2, but I'll try to push a bugfix update out soon!)