So what are you all doing when they inevidiably get thumped on and leave to heal and rest? Do you re-populate the dungeon? Put it on alert? Just run it as is?
Well, I thought this first (ruined) part of the dungeon involved fairly disorganised and disparate opposition, so I pretty much left it as it was.
In Jzadirune, the dark ones seeing that the adventurers had killed the skulk retreated down to the fortress, hobgobelins were sent to see what was the problem, assaulting the group while they were resting at Keygan house in the night.
One hobgoblin fled and after that the elevator guards were more numerous, 6 ready to stop the intruders.
My players left the gnomish ruins twice.
The first time they went in they closed the gear door to the first room that is slightly open, which alerted the Skulks that someone was in the ruins. So the Skulks ran around and started notifying each other. Then the players hit a few traps and went through the rooms with the "piles of rags" that nearly killed them. Then they made their way back down south and by that time the Skulks had organized an ambush in the Great Hall area. Then they found the rat and the Skulk led them to the hobgoblin gaurds. By the end of that the party was in really bad shape. So they had to retreat. (It was pretty funny describing their progress as they limped through the city streets back to the Temple of St. Cuthbert all bloody with two unconcious bodies.)
I had Kazmojen increase the number of hobgoblin guards over night to seven in the elevator room while they were gone. Then the party returned with eight people (party of six + Fario and Fellian) and retook the elevator, but between that battle and the first room of the Malachite Hold the party was so badly wounded again that they headed back to the Temple of St. Cuthbert again like thirty minutes after they had entered the dungeon! The city guard watching over Ghelves locks were like "What is going on?! You guys just went down there like twenty minutes ago!"
But anyway, during the time they took to go back to the Temple again Kazmojen had all his guards summoned to the central chamber to stand watch while he dealt with his customer and and placed some in the hall with the pit traps who's job is was to draw in any intruders and deal with them. He even called in the animated spiked chain. So most of the Hold was devoid of any opponents when they returned. Well excpet for the Main Chamber with Kazmojen.