If you complete Dark Agartha within 1 min of reset (I completed, looted, left, and 20 to 30 sec after I zoned back into Agartha day change and “New challenges available”) the game will ask you what level you want to fight at the next day, but when you zone in the start point is already activated, and it appeared the monsters were all still dead.
To counter issues with disconnecting/crashes there is a 15 minute window in which your Dark Agartha instance is still active and accessible. Just need to wait 15 minutes after you finish the previous one, despite new challenges, to get the new seed.
Would be cool though if the new key were to override the previous instance.