evilbob
Adventurer
This is a good question. Personally, I would handle it this way:
Assuming you're running the module as-is, the only thing they're really missing is treasure: and other than some decent stuff in the secret room, the only real treasure is the footlocker in the cult leader's room in the dungeon. (Did they already find the stuff in the master bedroom in the house? It's pretty valuable. Also, the cultist quarters technically has a few things, but they're not a big deal.) None of the rest of the story is really worth retreading at this point. Sure, they missed some good plot points, but hey: that's just how it goes sometimes. That's what's nice about a pre-made adventure: they didn't skip any of YOUR hard work.
What I would do is hand-wave the rest of the dungeon. They've already done the climactic finish - no need to get down in the weeds for all that other stuff. Just say, after they get back up and discover whatever horrible things are now wrong with them: "you spend an hour or so searching the rest of the dungeon, and find a footlocker that contains [treasure from footlocker in area 34]. Nothing else happens and you find nothing else of value. You head back up the stairs." At this point you can either add, "and out of the house, which is eerily quite" or let them decide whatever else to do. Once they get outside, ding level 3.
Whatever else they missed, they just missed. They sort of skipped straight to the end so that's pretty fair. I'd still ding them to level 3 though, even without any more fights - they'll need it.
