Welcome to the Org, cosminus!

Quote Originally Posted by Cambyses II
The Pope can reappear in any of his former provinces, though a reappearing faction usually only turns up in one province, any nearby rebellions in progress may choose to join them. Also if any of their former provinces are rebel at that time, then they will probably rejoin their faction. I have seen the Papacy reappear in the Papal States, and not Rome, many times.

Somehow the AI keeps track of a province that rebels away from it's faction by civil war or by the faction being wiped out. Those rebels in that province will remember which faction they belonged to and return to it.
Yep, that's been my experience as well. Also, given that a re-emerging faction is more likely to reappear in rebel provinces (although admittedly not always), I tend to make a habit of grabbing a dead faction's good provinces but leave alone the crappy/mediocre ones.

This strategy allows me to pick up some decent lands, while at the same time reducing the possibility of the faction reappearing in my territory later on. (I'm particularly fond of doing this to the Almos and leaving them stuck in Cyrenacia. )