All that would really need to be done is to add some logic to the quest where it determines if the drones are alive or not. If not, after Epinone Lab and the CAU show up you just tell them "The Drones? Killed 'em a while back." or something to that effect.
SPOILER
Though in doing so you'd also end up killing a Protectorate agent, and Im sure the Protectorate would know about that.
