According to this post and its status-bydesign tag, if a question where someone offered and awarded a bounty is deleted, the bounty is refunded back to the bounty owner. In most cases, this isn't much of a problem - either there was no awarded answer, or the bounty awardee loses their award.
Today, on Stack Overflow, we encountered a case where a user somehow earned 1,000 reputation from a deleted post. While we initially dismissed this as just another occurrence of the above (the user had awarded two bounties worth 500 rep on that question), after some further investigation, we discovered something odd: the two answerers that had been awarded the bounty still got to keep their bounty rep. I then realized that this was because of the "statute of limitations" on rep changes from answers: if it has a score of at least 3, and has been visible for at least 60 days, any rep change from the answer is kept, because those deletions are usually unrelated to the quality of the answer itself.
A lot of users there complained that this was a bug, that the bounty rep shouldn't be refunded upon post deletion in general. But according to the above post, this is intentional and by design. However, I request this behavior be changed in one case: don't refund the rep from bounties where the answerers would get to keep their rep due to the statute of limitations. Without this, you can have two copies of the same rep that the bounty owner spent initially and awarded, with one copy refunded due to the question being deleted, and the other kept by the awardee due to the statute of limitations.
There are many reasons why this should be done. First, this has a very high potential for abuse. The bounty rep is now doubled in the system, and the rest is obvious.
Second, it doesn't make sense to me why rep changes from bounties are included in the statute of limitations for answers, yet excluded in the same for questions. It would make sense to have them both included, or both excluded.
Finally, while this issue can be resolved by also excluding bounty rep changes from the statute of limitations for answers, I think it's fair to keep them included because, as I said, such deletions are usually unrelated to the quality of the answers themselves.