I had a bounty awarded for an answer I gave. After I deleted said answer I still retained the bounty award (ie: total rep not subtracted), even though the rep audit is showing a different score (ie: without the bounty).
Is this intentional?
If your reputation audit is showing that you are losing the bounty reputation, then you are losing the bounty reputation. Deleting a post does not cause a direct effect on your displayed reputation, requiring a reputation recalculation to update it to the correct value. This would be the same as if you gained/lost reputation from votes prior to deleting a post.
The rep audit is the real reputation.
You are out of sync, but will get re-synced when your reputation is recalculated.