In general, rep gain and loss for questions and answers that are deleted is gone - it's as though the questions and answers never existed.
- How does this work in relation to questions where a bounty is placed on them, and awarded?
My guess is that everything reverts - the question asker gets their bounty rep back, and the awarded answerer has their bounty removed (both changes only occur on a rep recalc, though).
Not sure what made me wonder about this, but now I'm curious, and am thinking that if no one knows (or is willing to divulge) the answer, then a test ought to be done.
It's also yet another reason to avoid frivolous bounties...