In a mission where you need to steal shipment of energy shileds for Gorsky on Domination, you can't eliminate all personnel in the warehouse, because when you attack Protectorate Dreadnought (at least it was like that in previous version) whole faction goes hostile, no matter if you walked out of main gates or through ventilation.
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Now it's cptn Wilkins, after his elimination everybody in warehouse goes hostile - outline is red - and guards outside (Private Lloyd etc).
I remember for sure I could eliminate everyone inside warehouse without causing hostility on Hard e.g.
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I'm pretty sure the elimination even of one real Protectorate military personnel causing hostility, you can safely eliminate workers and supervisor.