I dunno... I'd kind of lean on the side of them thinking the lights just went out, rather than them thinking their that their bodies were just picked up and deposited elsewhere.
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I am not really against an automap that marks down what the party perceives; even marks the traps they detect, but haven't disarmed. My concern with that though, is that IMO the automap should incrementally refine itself while they are in the area**, starting with cursory details; such that running through halls in a blind retreat, doesn't net them a fully drawn map that details everyplace they passed through.
**It could even be done statistically, via stat checks while they explore. It was the case in Lands of Lore that PCs would notice secret doors; and I think it was in M&M?? that PCs would notice collectible loot in the area, or even on tables; the stuff would only appear once they'd seen it. I wish the traps in FO3 had been like that.