Taking Out the Armored Skulls Non-Lethal (Very Poorly)
Yes, I know it doesn't count as a kill even if you do take them out lethally. As aside note, I tried just crawling around and having Quiet cover me, but the Skulls eventually do enough damage to her that she has to return to MB.
They'll temporarily group altogether and shoot at you, and after a short period, you'll only be fighting 2 at a time. If you only see one and don't spot the other, there's a good chance a giant rock is being summoned and ready to be hurled at you from a distance or even from higher ground.
Take them down to passed half-health and they'll build an invincibility bar that fills over their health bar; I don't know about doing this battle lethally as I didn't have any lethal loadout, but only way to damage them if you're going non-lethal is to counter them with CQC when they pull out their machete. Ideally, wait for them to both pull out their machete, run up to one and then just wait for him to teleport melee you in 1 of 3 ways - from the air, which requires a much quicker R2 prompt, or ground, which has quite a bit of delay (one of them might be so far that you should run up to him in fact).
After a CQC counter, if you stand right next to them, they'll teleport attack you again - the best situation is when they both have their machetes out and are both next to you since you can continuously counter both (example at 8:38). Once their invincibility is down, try to focus as much damage to one as you can since after you remove their armor, they'll charge it back up again.
The more annoying situation is when you're trying to counter one and another one summons a ground rock under you - you have to run since these blow up. Every now and then, all 4 will regroup - find cover as usual, keep an eye out for any duo who may be hurling giant rocks at you, and eventually it'll just be you against 2 random Skulls.
In case you're wondering, despite this sad display of skill, I received an S-Rank on this mission.
METAL GEAR SOLID V: THE PHANTOM PAIN
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