I can't confirm it, but I read something in another thread about the trainer sometimes causing NPCs to vanish. I think it was the "easy level up" function
The trainer i used onley worked for gold and ordenary fighters, the bosses you had to kill them on your own. I know that in the beginning some npc's vanished and i had to restart the game with only gold option and life. So yes i do think if you uses easy level up the NPCS vanish, that's why i didnt use that option.