That just looks like you have something set up wrong (if it works everywhere else, it should work anywhere). Put an event in that sets your flashlight object to the back of the layer just to make sure it's never anywhere else no matter what you do in C2. I mean, I can get light show "show through" further on up if the light object overlaps the shadow boundary, but that shouldn't matter in your game's case.
If you're looking for an alternative, I wouldn't jump things around layers--that sounds like it'll come back to haunt you later. I suppose you could always place a black tiled background on the floor above (and below depending) that stays locked there until you switch levels to hide anything.