Adam Lear has been digging into the circumstances behind this feature request, and determined that the behavior described there is likely an oversight: it should not be possible for a bounty to remain both awarded and refunded when a question is deleted.
Reputation removed from those who've awarded bounties on deleted questions where the award is retained by the answer's author
So we've patched that up: starting today, when a question is deleted and has had bounties awarded to answers, the bounty amount will be refunded to the person who offered the bounty only if it was not also retained by the author of the answer to which it was awarded (reminder that bounties don't migrate - they're always refunded to the offerer). This also applies retroactively to older deletions that were subject to the previous rules.
Once recalculated, this will affect the current reputation of around 4,000 users network-wide. If it affects you, I apologize for the disruption; please let me know if you observe a change not reflected in the bounties you've offered in the past.
New restriction on authors' ability to delete their own questions
While digging into this, we stumbled upon a more insidious problem: folks offering bounties on their own questions, awarding them immediately upon getting an answer, and then immediately deleting their question. This was allowed in cases where the answer had not yet received any upvotes and no other answers had been posted, and fortunately has been extremely rare... However, it is such an overtly hostile behavior that we've taken steps to block it as well: starting today, authors may no longer delete their own questions if a bounty has been awarded to an answer by anyone (unless that answer was already deleted).