But having an instance be something completely unrelated, taking all the meaning out of actually running it later on? That's ruining stuff for the newer players.
Haukke Manor was filled with imps and skeletons and all kinds of voidsent, just the way it is during the actual dungeon. Saying "
We sneaked around in a haunted house but didn't fight the monsters there" and later returning once you hit lvl..27 or whatever it is, to now actually slay the creatures that during the event you could just sneak past because you were still just a little beginner? That makes sense within the narrative.
The same can't be said about seeing a freed and cleaned up Dun Scaith City being readily available to everyone only to THEN be told "Oh btw, go clean it up, it's this unknown place filled with monsters that no one has ever reached!". See the break in logic?
You can argue that adventurers who have been to that place liked the look of it and tried to recreate it on the ground when they built their new housing area, but the OP asked what will/should happen with the place itsself, not a copy of it or something like that. And people moving into content that will still be relevant to someone down the line does not make for a good..well, anything, really. Because anything that is publicly available there breaks the story if it's available before clearing said content.