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Yea, most of the barrows/caves don't reset if they get the "Cleared" mark. There are a few exceptions, but there are so many different dungeons and caves you can always find something that has baddies in it.
Most dungeons do refresh, and it isn't always after a mission. I don't know when myself, but almost everywhere I go I have the interior cell reload all enemies/chests, although sometimes puzzles are solved where other times they aren't, which is odd.
Dungeons tied to the main storyline don't seem to reset at all, also dungeons with a "Dungeon Quest" don't seem to reset if they are "Cleared" or the quest is completed. This is just what I have noticed in my playthrough, with the different glitches that
occur I am sure people see their games performing differently.
same as chainSmokingBob on my game being cleared hasnt meant much except ive been there already, went back to a "cleared" dungeon to get some loot i left behind (maybe a couple in game days) and to my surprise i was being attacked by bandits again. theres
a castle in front of riften that seems to refresh just every couple game days.