I'll start by explaining the vanilla hunter system as I understand it. When the player character enters a hub map, or violates the masquerade on a hub, the spawning conditions are checked. And if the conditions are met, the apropriate hunters get spawned. Whenever a hunter is spawned, the triggers to teleport him at the attack places get activated too. It's not the best system I can imagine, but up to here, it works.
Now when the player hits one of the triggers, the hunters currently on the map are teleported to the connected ambush position. And starting here, it gets messy. The triggers stay active until the hunters spot the player and go into combat/ pursuit mode. That also disables the teleport triggers. But if they lose contact, the triggers are reactivated. So if you cast any not instantly deadly Dominate or Dementation level, or Song of Serenity, the trigger is reactivated and usually the player is still in the trigger area, so the hunters are immediately teleported back to their starting position and reset, so the discipline effect is lost.
Here's where I have changed things. Now, when the player hits a trigger, the hunters are teleported to this ambush point, and the triggers are diasabled until the next hunter is spawned. So if for some reason, you don't kill them but try to get away, they will come out and search for you.
And while I was on this, I have made some other changes as well. First I have further increased the spawning. With humanity 5 or less the first hunter will appear at 1 violation. This has been in CE for quite some time now. But now I went even further. For humanity 3 or less, a hunter will turn up even if you don't have any active violations.
The other change is the handling of killed hunters. In vanilla when you kill a hunter, no more of the same level are spawned until you travel to another hub. Now for CE if a hunter can't be spawned because of the hunter dead counter, there is a 50% chance that the counter gets cleared.
So you violate the masquerade twice, or once at low humanity, the hunter chick is spawned. You kill her. In vanilla that's it. no more hunter chick until you go to another hub. In the next CE version, you go to a submap and return to the hub, or you violate the masquerade again, there is a chance that the counter is cleared. And if that happens, at the next opportunity she gets spawned again...