It depends a bit on your timing, I guess. There are not a lot of quests that involve magisters directly, IIRC, except, and this is a big one, Ifan's quest with Magister Borris. The other one that I can think of is the gheist on the beach and his flowergirl. I'm pretty certain Larian has put in a failsafe for Ifan's quest (e.g. a note on the body, or a bodypart you can eat), but... no guarantees.
I guess ultimately the basic rule of RPing holds here as well as anywhere else: Make sure you complete all sidequests before taking that final step that closes off the area
