You lose Humanity when you kill a hunter ONLY with a stealth kill and ONLY if they're not aware of you. Creeping on them, then stealthy feeding on them and killing them that way, doesn't make you lose Humanity either.
If they engage you in battle and then you do a stealth kill on them, you don't lose Humanity, which is stupid, you should either always lose it when you kill them, or never lose it, and just that it's situational thingy.
And I'm fighting them in an alley where noone else is around, so it's only 3 of them and me, and it shouldn't violate Masquerade, and since I'm not using Disciplines or feed off of them anyway, it shouldn't be anything other than Criminal Violation.
However as I said... since with CE they increased numbers of hunters and spawning points have been changed from my understanding it did create a problem. Especially since unlike other havens, the first one has very small one way alley leading to it. And you have to engage them in combat to pass them.
Also... I'm not sure if it's the same thing with Masquerade with non-modded version of the game, or if problem arose with TCI changing things about hunters.
Yeah... I don't think that they've changed anything about Masquerade and Nosferatu either, but something may have gone wrong when they changed hunters. And I can't test it, since I don't have space on my comp to make another installation, just so that I could test it (also... conditions to trigger those naturally (as in without cheats) do take loads of time).
But yeah... even tho CE had it's Final version, I should have posted there... Which I'll do now X_x