What everyone else says. There is no onscreen scene where he's officially given the position back - he just starts doing it again. Given both Morgan's concerns about Hotch, and his reservations in taking leadership from him, I think it's safe to assume that Morgan was more than willing to give it back, and no longer thinks Hotch is going to commit suicide by BAU.

If there isn't a missing scene fic for this, someone quick! Go write one.