I thought the environment might matter too (eg: left out in the rain versus under cover), but from the ~25 hours I've put into Ground Zeroes there doesn't appear to be any consistency. A semi random knockout factor might exist, but yeah, as a whole I think it's more likely a processing/memory issue, the engine struggling (or simply not optimised) to keep track of all guard status.
Definitely had knockout soldiers completely disappear though. It's so weird. Their guns are usually still there, but no body.
I definitely feel like that stuff is a hold over from the console versions because I remember playing on the PS3 and collecting guards thinking "This loading guards in and out thing is really inconvenient, but hopefully that will be way better on PC." But it was exactly the same.
It'll probably be better in TPP, or hopefully people will figure out what controls the timers/numbers that handle guards in different states.
The only case I've had of guards permanently despawning is when I was abusing alert and causing more and more reinforcement guards to come in (Because they always had better stats in PW) and when I got up to 75 or so guards, the game was struggling with loading them in and out as I ran around despite their "marker" being on my map, and after awhile when I had too many guards and took too long to get to them, they did eventually start disappearing for good with only some of them returning once I had extracted a whole bunch.
When collecting guards I work in sections and keep morpho at a LZ basically the entire mission, then as I clear out more convenient Landing zones I bring him in further.
It takes awhile and requires a ton of running around but you never have too many guards knocked out or at risk of despawning if you're extracting them area by area.
Well back in February 2014 they said that certain things would carry over.
And then there is this (bottom two)
Sadly it's not made clear if that is referring to the POWs that you saved or just the bonus Mother Base Staff that they recently announced.
So far any character you extract with a yellow text, POWs, Unique Guards and so on will be what carries over to TPP
What we don't know yet is if regular guards carry over, but better to be safe than sorry.
It kind of annoys me the PC version doesn't get any of the CE or Day 1 version bonuses, even by pre-ordering.