I know about a few of the non-lethal options, but it just so happened that in the Golden Cat mission I was in stealth up until I accidentally walked in on one of the brothers...he saw me so I had to kill him, rendering all the sneaking around I did useless as every guard somehow knew I was there and I had to completely leave the building before killing the other brother....Which resulted in me having to kill more guards than I wanted to just to protect myself. I am wondering if there is any way to still choke out or silence a AI once they have already seen you? This is a problem because I run out of sleep darts a lot (I wish we could hold more than 10). The small amount of ammo held forces me to use sleep darts from above or when a AI see's me and I am far enough away to not have to kill him for him to shut the hell up and alert others.

Is the only option killing once they see you? Or is there a way..sans dart to choke them out once they see you.

Run away, wait for their awareness to drop below murderous rage and wait patiently for an opening. Otherwise, no I don't think they'll let you choke someone out while they're trying to kill you. It'd be very hard to get positioned behind them though to do that while they're aware of you.

Unless you have Stop Time or maybe Bend would be enough. I wouldn't know about that though.

Maybe Time Stop and get behind them.... Otherwise I don't think so.

You can blink behind an "aware" enemy and choke him. But it has to be fast.

Non-Lethal takedowns don't work in my opinion for one simple reason.

I was running around in a certain level, and I happened to linger more than I would have (couldn't figure something out because I forgot about an entry point), and when I looked over with the Sight ability to see through walls, I see rats freaking EATING the UNCONSCIOUS GUARDS that I took down.

I mean, wtf? How am I supposed to get through something without killing anyone when the rats are doing it. I know it was counted against me, because in one level I killed a few guards (all hidden high on pipes), and choked out/sleep darted 8 guards, and after the mission was over, it said '11 killed, 0 bodies found'.

Please fix this Bethesda. I love the game, but this feature doesn't help me get the achievements for not killing people (not counting Ghost right now, as I'm not that great non-lethally yet).

Don't throw around unconscious guards so easily, they are fragile. Maybe you didn't treat them well enough.
I killed a guard once by pushing him gently down in the water.

I only had rats eat someone once.... though I suppose the prevalence of rats depends on the As a precaution, though, toss unconscious bodies onto elevated surfaces (desks, beds,
boxes...etc) where rats can't get to them.