We've been getting a lot of questions like this ever since the feature to see event reversals such as deleted posts and serial voting was added into the reputation history; and their confusion is legitimate. Even well-respected users have become confused by that number above the day. It should display the reputation changes for that day.
I propose that reversal events such as these be visually separated from the main events for that day and not included in the total reputation change for that day. After all, their reputation isn't actually changing for that day, but reversing changes from previous days. These events already seem to get bumped down to the bottom of the events for the day, why not add a simple separator between them?
Events indicating reversals
Events which have been reversed
Perhaps a second, smaller number could be added next to the main one to indicate that other events took place on that day, but I feel most users who really care will have noticed or went looking for the events anyways. However, including them in the actual change only serves to confuse people.