I have a seen with basically 2 sets of geometry. I want to lightmap each set separately. So I turned everything in the scene on, lightmaped it, locked the atlases. Then I turned on only one set of objects selected them and baked selected. Then I did the same for the other set. I thought since I baked the entire scene first and locked the atlases, then selected objects, I would be able to re-bake just those objects. It didn’t work. How do lock atlases work and what would the workflow for this be? Thanks.
Hmm, it seems that “Bake Selected” just ignores the Lock Atlas setting and does whatever it wants 
You should create a bug report.
I don’t know. I’ve tested it with both Bake Selected and Bake Scene with each set of gameobjects selected/visible, same results. I’m beginning to think that the locked atlas only holds if it’s part of the each bake. The documentation says it holds the current atlases if you add objects to a scene, not remove them from the lightmap bake.
So my next question is can I bake selected and not have the un-selected gameobjectes effect the bake, not cast shadows or add AO? Thanks.