Any know what happens if a religious supremacy/league war is fought and won when the winning faith isn't represented in the empire at all? Does the empire go to the league war leader?
So you're saying that the protestant league started (aka, Protestant elector vs Catholic emperor). The war starts and then you swapped all of the religions in the HRE back to Catholic mid-war? And in this situation, the Protestants win but the new emperor is a catholic HRE nation?
Interesting. I wonder if you did that and left a tiny country like Mantua as Protestant, if Mantua would get it?
I assume what vleup said, Protestants winning simply boots the current emperor and gives every losing nation some temporary -1000 elector voting modifier and then let's the elector vote happen naturally.