Inverse of isvisble added to your conditions works great when using nonvisible layers and mouse on object clicked. Yes, it's one extra check, but it's a lot less work than trying to save the state of your game and switching to another layout.
Are you sure one would even need to save the state of a game?
Couldn't one simply use global objects (arrays, variables, etc)?
Either way, I think I'll need to scrap the idea of using layers. It would be way too messy and complicated for my editor suite.
For one, I want to set up V as a hotkey within the scene editor. While pressed down, this hotkey would remove (in terms of visiblity, not game logic) all buttons and only show the test character and the background scene (sans the blue lines seperating the walkable area from the one that is not).
I'd essentially need to split the layers at this point, which isn't that great either