It was destroyed only 1 center of reformation.
Here is a save of the game i was playing now.
More than 20 years earlier, there was a 3rd protestant reformation center in south germany that got destroyed, the other 2 continued converting land.
Now, recently Denmark just converted to protestantism (it was not forced by war, and didnt noticed any rebels there), but no religious center apeared there.
Had already observed similar stuff in recent games and found it odd.