I periodically restock my GURPS DF dungeon. I have two broad approaches - restocking, and reinforcing.
Restocking is seeing if the dungeon's empty areas have become less empty.
For re-stocking, I pretty much just re-roll on the stocking table for rooms that have become empty and see if the contents have changed. If the roll turns up "monsters" or "special" then monsters have moved in or something noteworthy is now within that encounter area.
I don't always roll. If a change is logical and adds feeling and depth to the dungeon, I just do that.
What gets added depends on the keyed area itself - a big room might get a big monsters, a small room a small one. Corpses might be torn apart but have attracted rats. Corpses may have risen as undead or spawned a ghost. Entirely new monsters may have taken up residence.
Sometimes I just don't know so I roll on my Wandering Monster table for the area and moved that into the room - maybe the orc patrol set up a picket area, the ooze stopped oozing for a while, the stirges built a nest on the ceiling.
Unlike restocking, which is essentially random, reinforcements is a reaction roll. For my purposes, it requires surviving monsters.
Instead of just making a random roll based on initial dungeon stocking, I make a reaction roll. I give bonuses for strength, goals (the monsters have a reason to be there), neighbors that have been weakened, success, and other positive modifiers that make sense for the situation. I give penalties for losses, stronger neighbors (especially if the monsters have been weakened and their neighbors have not), weak goals or no goals, and failures.
Of course if the center of gravity remains they'll stay no matter what, and if a load-bearing monster is slain the survivors will scatter no matter what.
On a neutral reaction roll, they maintain the status quo. On a positive (Good or better), they reinforce the area if possible. On a negative roll, they'll pull back or pull out entirely, or pull back to a safer area.
Naturally, if they pull back or pull out entirely, they'll take any movable treasure with them and may hide or trap what remains.
In short, I look at it two ways - same the initial restock, just seeing what's there; and rolling to see if the locals react positively or negatively to PC actions.