Jeffries appeared again in the Bendis Ri Ri Iron Man book
I think there is a small chance of him getting killed.
This arc is about an alliance of criminals led by The Hood attacking Doom-Iron Man. Some years ago Jeffries had a House of M story by Christos Gage in which he was a South American dictator, and he was killed by The Hood leading an alliance of criminals. Perhaps Bendis read that story, and since he is a D list character not that many people would care if he gets killed (I would)

First page is the Iron Man book

The House of M story
House of M - Masters of Evil 003-011.jpg

I think Dr Nemesis has been in Limbo since Spurrier's X-Force, he should have been seen during the Terrigen Mist period looking for a cure.