I was investigating a change in my reputation; I got -4 points but it doesn't show up in my reputation summary on my User page. The more detailed daily view tells me that I lost the points due to someone else's post being deleted; I had reviewed the post.
At first I was confused by this, since -4 isn't a listed amount that can be gained or lost. I trawled through my reputation history and eventually found the corresponding post, I had my answer: I had edited the question twice and both edits had been accepted. So the -4 is rebalancing that. All good.
So: should this way of losing reputation be more explicitly listed in the "What is Reputation" help page? Currently it says
If a user reverses a vote, the corresponding reputation loss or gain will be reversed as well.
Obviously the intention here is the same as in my case. I just don't think that it's apparent that reputation changes due to a particular question (or answer, I'm guessing) can be lost if the question or answer is deleted. It's logical that they should be, it's just not apparent.