Moderators can refund the bounty to the users offering bounties. (However, this only happens in some rare situations.) If that happens, can we see this in the timeline and revision history? Is some event recorded in the PostHistory table in the Data Explorer?
Based on what I read in the FAQ post "How does the bounty system work?", it seems that the bounty simply disappears without any trace. But it is just mentioned in passing, I wanted to get some confirmation on this.
However, diamond moderators can clear bounties, which would effectively remove the bounty and clear its history. The bounty owner's reputation would be recalculated as if they had never placed that bounty. This would then allow it to be closed, migrated, or deleted like any other question. (source)