After I receive the new objectives a death scene arrives and I lose the mission with this final information:

Don't kill anyone

And yet I didn't kill either the guard in the beginning or Raul who gives you the map and key just before this happened. I did use the Blackjack on the guard but I never managed to do it from behind so he didn't went down with one blow but according to the wiki it deals minimal damage and he didn't die when I finally got him unconscious.

If anyone has a save during this part it would be very much appreciated if you could upload it but requirements would be New Dark 1.21 with Thief Gold, TFix 1.16a (if that matters?) and at Expert difficulty.

Nevermind. I replayed the mission and this time I didn't bother with the first guard (it's freaking impossible to steal his key without him noticing it) and now I'm at the place where you get the new objectives and I can continue.

if you still have that save where the mission fails, do share it, I'd like to have a look - maybe there is some environmental hazard that is killing the unconscious npc or something.

I know you already got the problem figured out, but I just wanted to say that it actually is possible to kill guards with the blackjack. Even though it doesn't do a lot of damage, if you hit them with it enough, they'll die. Usually, an easy way to know if you are close to killing someone with it is if they stop fighting and start to run. After that, it only takes about four or five hits to kill them. Granted, I don't know if the guard in the tower would have tried to run since he was alone.

If you already knew that and considered it, then it probably was just a glitch. I think I read somewhere that a glitch can occur, though I can't remember if it was from knocking the guard out or killing a Crayman.

I didn't know about that, but he didn't start to run but he didn't take a lot of hits before he went down which is why I didn't bother with him after my restart. In my restart I actually didn't use blackjack once in the entire mission, wanted to see if I could do it without as I've been abusing it once I got angry in a situation where it felt as impossible as stealing archer's key in the beginning of Song of the Caverns.

It's likely a glitch though because I didn't receive the failure right after I knocked him out, I received it when after I got the new objectives later in the mission. The weirdest part was that according to my stats that followed was that I had neither killed or knocked out a human at all.

Okay, yeah, that sounds like a glitch, especially if your stats didn't show that you killed anybody. At least you got it figured out, though.

more like "something came and ate him while he slept".