It appears that reputation earned from editing a question that is subsequently deleted is not subtracted in a reputation-decreasing event (e.g. a "-2: edited question was deleted") that shows up in a user's history, but disappears into a memory hole, seemingly never having existed in the first place. Is this the intended behavior? And if so: why shouldn't this show up in the historical record (like the loss of reputation from votes of a deleted user)?
If you check the checkbox "show removed posts" on your reputation tab, you should see also the reputation lost when post with your suggested edit was removed.
You can check the section "My reputation dropped, but I don't see anything listed!" from the relevant part of the FAQ post How do I read the history of my reputation? This bullet post is most likely relevant to your situation:
Removed posts are hidden. More than likely, you don't have your reputation history set to show removed posts. By default, removed posts are hidden from the history pages. In order to show removed posts, you need to make sure the checkbox all the way at the bottom is checked.
Just to add a (kind of) experimental verification, I will add that I can see this in my reputation tab here on MathOverflow:
I will mention two more things. (Based just on observation - I did not try to find whether this is documented somewhere.) One is that this kind of reputation loss is not shown to other users viewing your profile. The other one is that next to the number showing the reputation loss I see only the title and not the link to the question - this is related to the fact that I do not have sufficient reputation to see deleted posts.
When I found similar reputation loss on another site, where I have enough reputation to see deleted posts, the link to the post was available too.