Deletion of a user removes all of their votes and accepts. So not only would you lose the acceptance bonus, but anyone who was voted on by that user would also be affected by the removal of those votes.
Merging does delete one of the accounts, but it does this after attempting to transfer votes and acceptance ownership to the target account. This will generally mean that acceptance won't change, but votes might change if, for example, the user voted on the same post with more than one account.
In addition to deletion of votes, additional reputation changes may be observed due to the deletion of user accounts - content with a sufficiently low score is deleted, which may refund your reputation if you had downvoted on such posts. Additionally, bounties are reverted from this action - you can see this from the lack of the bounty history on this question that was pointed out in an earlier bug report for the old bounty system.
Reputation is handled in the same way that it is handled for deletion of posts - your displayed reputation is a denormalized value that isn't updated. A rep recalc that you can trigger at the bottom of your reputation audit will reset your reputation to the correct one.
To my knowledge, there's currently no definitive FAQ on this - all of our account deletion posts on Meta seem to be more about how to delete them or on various bugs that turn up due to their presence, rather than the implications of being deleted.