You just have to reassign them again for the new layout.
So if you have an object called "Plane" that is global and on layer "Game" on one layout
Then when you load a new layout, you just add:
Plane move to layer "Game"
Was that what you meant?
Yes. Although I was hoping an automatic workaround was made. Seems odd that it's not provided by default.
Thanks though. I'll probably end up having to do that.