I've made a little test, because I experienced similar problems in my game.
Save the game at some point in time. Switch visibility between 2 layers. Deactivate group with event sheet code for invisible layer. Load the initial save from before the group deactivation. It seems that the game is loaded, but the group is still deactivated.
Am I making a mistake or is this not supposed to happen?
Edit: remember to save before pressing switch, otherwise there will be nothing to load, and the game will just be deactivated.