I have down voted and flagged two answers as "not an answer." Doing so reduced my reputation by 2 (1 for each down vote). It seemed both of my flags were helpful and both answers were deleted.
As requested, flag screenshot:
As far as I can remember, when a down voted answer got deleted, we got our reputation back.
So I did by manually re-calculating. You do not have to re-calculate yourself as it will automatically happen at some point.
Rep regain screenshot:
This information is either very hard to find in the FAQ or SO Help Center or Meta Help Center... or it doesn't exist. It only mentions that you lose 1 rep point for down voting answers, but it doesn't say that you get it back if the answer is deleted. It's commonly known by more experienced users but think about new users, or the ones who are not aware of it...
Let everyone know that voting bad answers is a good thing! That temporary loss of 1 rep point will be given back to you in case the answer is deleted.
Based on the above, I think the FAQ and Help Center should be updated.