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I started a new alt a few days ago. I was making all sewer quests and bang! In Fetid Halls Dr. Noxious and its minions are missing. Enemies count is 24, that are the enemies defending containment units; killing them all terminates the level and still no trace of evil doctor. Did something go wrong with the latest update?
He was already killed. You entered an instance where somebody already killed the boss and left. When in doubt, exit through the door then come back in. Makes a new Halls instance for you. This works for any of the quest instances.
If you entered from a hosted instance you had previously done already and never entered Halls then I dunno.