I happened to be looking at my profile on Interpersonal Skills recently, and I saw that I have 103 reputation. I also saw that I had a +4 reputation change since the last time I had checked:
This was quite surprising to me. I had started off my Interpersonal Skills account with an association bonus, which means that I originally had 101 reputation. I have never posted a question or answer:
Thus, I cannot ever have received a downvote. Nor Can I have ever cast a downvote, as I have not reached the privilege level of 125 reputation for that. So in order to have 103 reputation I would have had to earn +2 reputation which could be easily explained by an approved edit. Indeed, when I expand the reputation tab, that is what I see:
So how is it that I have earned +4 reputation if I only have 103 reputation, and one approved edit?
Some further digging led me to click on the "show removed posts" box. Voila! There was another approved edit where the post had later been removed:
So it turns out that I had earned +4 reputation but I had also lost 2 reputation when the post was removed. The only problem now is that the notice of reputation earned since my last visit, and the number displayed on the reputation tab (see first two screenshots above) seems to only have realized that I gained 4 reputation but does not seem to realize that I subsequently lost 2 reputation. Instead of showing me that I gained 4 reputation it should show me that I gained 2 reputation.
Now at this point I figured that maybe this is simply status-bydesign and for whatever reason the notices only show the reputation that has literally been gained and ignores reputation losses. Indeed, the answer to this similar question argues exactly that:
The tooltip of the box explains it all (emphasis mine):
Reputation gained since your last visit to the reputation tab
However, further research showed this to be incorrect. On another site, where I had recently received a downvote, it did incorporate the -2 reputation into the total "reputation gained":
As you can see from these screenshots, it says that I have earned 233 reputation since my last visit, with 128 reputation in a particular tag. These numbers only make sense if you count the -2 for the downvote shown in the dropdown. (I.e. add up everything up to and including the +20 under "yesterday" and you get 235 if you ignore the -2 and you get 233 if you include the -2.)
Thus, it is established that the number shown for reputation gained since last visit does incorporate reputation losses. This being the case, it should also incorporate lost reputation from reputation gains on removed posts. (Note that the graph completely ignores the gain and the subsequent loss from the edit to the removed post.)
I found this related question which asked about such a discrepancy within the reputation dropdown list itself. It is status-completed and indeed when I uncheck "show removed posts" it hides both the gain and the loss. So it looks like that was fixed, but for some reason it doesn't carry over to the total summary which is still only incorporating the gain but not the subsequent loss.