What I am assuming happened here is that the content was deleted while you're still on 3.x and something happened there to cause the disconnect. As we now handled that differently, the software is unaware of these abandoned images and won't deleted them because they aren't tied to content that was deleted on version 4.
If that is not the case, we can investigate further. However, what you're in the middle of now with transferring these, is probably the best way to clear them.