I have the same issue too when up to some point I need to copy the layer to most of my layouts but not all. Global HUD is different thing (I'm aware of this), my problem is when I get a layer setting/properties/effect right, I want to implement them to all levels and minor tweak (position, add sprites, etc) them individually. Seriously if there is a feature like it would cut a lot of production hours.
I hope this thing is in the Ashley to-do list or will be in the list at least.
hours ? how many layers are you talking about :P
Just a hand full of settings per layer ... and even with 20 layouts, adding and chaging the layouts should be easy.
I feel this is more of a degsin approach flaw ...
You create several layouts, probably for levels, then started working on one of them and expanded it a lot ...
As it sounds, the quickest option for you would be:
Duplicate that one layout you made furthest.
then clean out that duplicate, retaining the layers, then copy the objects from the older layout which require the adaptions, to the new duplicate. From there you can select ranges of your objects and shift them to the appropiate layer