proper lighting building workflow question

can someone explain to me a bit the lighting building process?
my level (persistent) has a bunch of different levels in it(like different sets of environments, but because of the way theyre built, they have overlapping locations, and different suns and skylights).
i thought i had to turn off visibility on every level i dont want to be part of the baking,
then turn the baked ones visibility off and turn the next set and so on, but it seems like somehow if i do it this way, it complains about the previous level i built lighting is now “lighting needs to be rebuilt”
what am i doing wrong?

just to be clear, these sublevels are not all loaded at once, i unload the other ones etc, so there shouldnt be any time with 2 direct lights or skylights in the game at the same time.