The Dungeon is going to be reset. No idea about the sentient NPCs. Rememeber she said that they were somewhere else preparing for a war before they got transported here and given a command to protect the place.

A dungeon being reset could well mean that the environment gets reset, and monsters get transported back to wherever they belong to, only to have them re-transported to fight once a gate opens up once a player or hunter joins again.

The fact that they glitch etc suggests they're part of some digitized system. At the very least they can be controlled.