What is the best procedure when deactivating a user in Workfront regarding open proofs -- re-assigning or removing them from proofs in the Workfront Proof Tool? If you remove them from the proofs, does that remove their comment history as well?

We remove them from all active proofs. You have to find that option in the contacts section. That leaves their approval on all old proofs, and their comments on all proofs, but doesn't hold up anything by leaving them on with decisions still pending.