I think maybe the state of the spirits in the Nest depends on how much the soul eater has fed on them. We don't know how often or how fast it consumes things, or if their rate of consumption correlates in any way to the deterioration of their bodies in the real world. But given the episode, I think it's more than likely there's no direct one-to-one correlation, since the consumption happens in the nest and therefore outside of time and space.
So the soul is outside time and space, but still lunch; if it is devoured (which most are as no one stops the soul eater) then the body dies, and the little bits of soul stick around and look sad and scary. Assuming a non-correlative rate of consumption to rate of body deterioration, we can deduct that it had abducted but not gotten around to eating either of the newer families or Bobby and Dean.
Then Rufus trapped it, presumably preventing access to the nest; which meant Bobby and the older family didn't get devoured, but their souls were stuck outside of space and time. When the new family released it, it started gnawing on them (hence the victims' beginning to deteriorate in the past and present), but is killed by the boys before it can (thus, the deterioration is halted and sets of victims wake up). So the two families and hunters were able to return to their bodies.
And the kids could see sad people because either a) they had been there the longest (having been grabbed first) and it takes either time to adjust OR a certain amount of soul-nibbling to see them; or b) kids are always more attuned to seeing spirits and stuff.
I think the biggest question I work up with was: why didn't they pretend to be from the CDC like they did with the Striga, because they would have had a better explanation for being there AND precedent in investigating strange coma victims.
Well, if they'd been CDC (which you're right is a better idea) they wouldn't mirror Bobby and Rufus. Unless of course Bobby and Rufus were also CDC. I got nothin. Maybe they lost their fake CDC IDs.
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My thoughts on timey-wimey stuff
So the soul is outside time and space, but still lunch; if it is devoured (which most are as no one stops the soul eater) then the body dies, and the little bits of soul stick around and look sad and scary. Assuming a non-correlative rate of consumption to rate of body deterioration, we can deduct that it had abducted but not gotten around to eating either of the newer families or Bobby and Dean.
Then Rufus trapped it, presumably preventing access to the nest; which meant Bobby and the older family didn't get devoured, but their souls were stuck outside of space and time. When the new family released it, it started gnawing on them (hence the victims' beginning to deteriorate in the past and present), but is killed by the boys before it can (thus, the deterioration is halted and sets of victims wake up). So the two families and hunters were able to return to their bodies.
And the kids could see sad people because either a) they had been there the longest (having been grabbed first) and it takes either time to adjust OR a certain amount of soul-nibbling to see them; or b) kids are always more attuned to seeing spirits and stuff.
I think the biggest question I work up with was: why didn't they pretend to be from the CDC like they did with the Striga, because they would have had a better explanation for being there AND precedent in investigating strange coma victims.
Re: My thoughts on timey-wimey stuff