Somehow I crack the code to see when all the dragons are lulled asleep, and when they are all asleep, I sneak in and swap the loot with Fluttershy. This has also the effect of disarming the dragons, since they then get scolded by her should they attack her at all, or keep her.
I put the loot in the vault full of Tank infected and various tanky units including War Elephants, Elephant Archers, tanks, Starbound bosses and the like, before also making sure it's an instanced mission so no one can teleport freely.