kilver

Another wild guess: does he have an item that grants him invisibility of sorts? You could check whether he's still there by applying an area spell that would cause him damage in case he's invisible.

OMG thank you! I took off all of his items and rested, then removed him and he was still standing there, so it must be it! (I checked the option to send him to pocket plane, and it works too). Or he decided that leaving unequipped is not in his best interest. Anyway, it worked, thank you so much for your help.

This is a wild guess, but how did you change him to neutral? What does he say when being kicked out, could you quote his line?

After being resurrected (Bodhis abduction) you have an option to change his character. And he says "One must assume that there is some logic behind asking such a skilled wizard as I to leave... but I shall be damned if I can figure it out."