When a truce is in place, guards will be posted at the entrances to the three storerooms. Continuing past a certain point will re-start the fighting. It's hard to pick this Dungeon clean before a truce is declared; there's a good chance that you'll find Arion Hunter before visiting all the other rooms. It's just as well, really, since there's usually too much loot to haul away in one visit.
But you will want to clean out all the storerooms, truce or not. You can use Invisibility if you'd rather not fight.