I hear the DLC is quite heavily bugged when it comes to properly importing choices.
But this issue must be a particularly nasty glitch if you "did it right" and he still betrays you.
Chances are in those 2 years Bull was reeducated and any empathy he might've had went the way of the dodo so really the Inquistor brought it on themselves.
Oh yes, very good point. They would absolutely have re-brainwashed him as thoroughly as they possibly can after seeing him almost "go native", hesitate to obey orders, and follow a thing's decision instead during his personal quest.
Edit: And since Cole can sense even very old emotions very clearly, I wonder if Iron Bull willingly submitted to the brainwashing instead of requiring any kind of coercion that would have left some kind of "distress-imprint" on him. A nasty thought, but ... it would make sense. I've big issues with the DLC, but this is definitely very fitting.