I would have left the second brood box above an empty super, the bee's may have moved the honey down. Then once the drones emerge and honey is moved take the brood box off. Although you do need to visit to let the drones out as they get trapped above a queen excluder if you use them.
It may be too late to save the drone brood depending on how long it has been off the hive, but you could replace the brood box above a couple of supers and let the bee's clear the stores.