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How does Skyrim determine if a dungeon is “cleared”

I just completed a quest for Falk Firebeard in which I had to clear Wolfskull Cave. I cleared it completely, returned to him, got the reward. However, it is not marked as Cleared.

Similarly with Brinewatter Grotto: I killed everyone inside except the friendly Argonian, and it isn't Cleared.

Both were used in quests (which weren't radiant AI ones) so I assume they aren't going to be reused.



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