I am adapting the adventures from Secrets of the Soul Pillars onward to my home brew campaign setting and have modified them to fit my storyline. Instead of Cauldron, the action is going down in the dwarven necropolis trade city of Hammerfast. The characters have taken down Vhalantru, and are looking for clues about the Fiery Sanctum. However, the players are completionists and have decided to check out Jzadirune to find a way down to the mysterious blank spot on Vhalantru's map rather than divine the way. I have three ideas of how to proceed. First, I could just say that other adventurers cleared it already, and let them travel-by-dot on a narrative journey through. Second, I could leave it as-is and let the 13th level characters mow through the encounters, which could also be a boring time sink. Third, I could try to repopulate the dungeon with level-appropriate encounters. I only included the lower level dungeons to fill out the setting so there was something to find on the map, assuming they'd use their considerable talents to find the Sanctum. If I were to repopulate Jzadirune, what would you fine folks recommend?
It depends on how difficult their adventures have been for them. If they've been challenging, curb-stomping their way through one dungeon might be a nice change of pace for them and having a chance to showcase their new (level 13 usually has some) abilities. In this case, I'd still punch it up above a first level dungeon. Bring the average CR up to 9 - 11, with a finale that's a 12 or 13.
If it has been a cake walk for them so far, go in opposite direction and make it a meat-grinder. The Vanishing was no joke, the highly skilled and magical gnomes had to abandon an entire city! Make the DC very high, and the on-set much faster. Maybe they vanish to the deep ethereal or the Far Realm, requiring a side-quest to retrieve them.
Jzadirune is a boring slog even by just the rooms. Don't do it.
Well, after some frustrating empty rooms, very dead bodies, and re-evaluating the purpose of their exploration, the intrepid adventurers realized their spontaneous casters hadn't taken advantage of switching out spells at 13th level. A find the path spell later, and they were back on track.