Originally I approach restocking as one would designing the dungeon. This was a mistake. Restocking dungeons shouldn’t feel like repeating work you’ve already done. The other issue is that of time, it is actually a necessary, active task, requiring doing. This is inconvenient and is often down far enough the pole to just be ignored.
I didn’t have any idea how to restock dungeons and research didn’t really provide a lot of insight. Nearly all of the advice boiled down to "Think about what would realistically happen next with the people in the dungeon." Is this an insight? Yes, in a megadungeon campaign, the dungeon itself is the stage the game takes place on, identical to the overworld map in a traditional campaign.
Can a space be cleared? Oh, to scour it clean. We love to eliminate the fog of war, till all is known to us. The nature of the megadungeon is that it can't be known to us. It is a representation of the unknown; the metaphysical darkness, into which we venture in an attempt to retrieve some vital forgotten knowledge and return with it to the tribe of man. The success of the adventure->treasure->level->adventure cycle is that it so naturally mirrors a hero's journey through life.
There is without question a resonance with that idea.
So, I don't restock a dungeon, as much as I treat the dungeon as a space in which adventure occurs. Here's what that concretely looks like.
The ProcessI ask for an encounter check when they are on a "thoroughfare" and moving throughout the dungeon, once for their movement times 10.
To unpack: No matter how you design your dungeon, certain areas will be the 'grass crossings' on a college campus. Players will just find themselves traversing that area due to it being the shortest route to where they want to go. It's also where you're most likely to meet random traffic, which the hazard die roll will certainly provide. Because the terrain is already explored, they've already poked and prodded with their 10' poles, they can traverse it at somewhat normal speed, 10 times their normal movement. So whereas an unencumbered party could explore 120' in a turn, now they can move 1,200' in that same turn.
Rolling one encounter for every 600'-900' (really 60-90 squares) encourages finding shortcuts and handles getting to and back from play at the start and end of each session. No party is moving around unencumbered.
That's most of it. We've got the other situations.
QuestsQuests are how I logistically handle restocking the dungeon. I have never in my life ever sat down and rolled to restock rooms. I don't think I have it in me.
Every area in the dungeon has. . .things. Resources. If an area's been explored, and I'm looking to "restock it", it initially happens with a quest. I have a selection of Non-Player characters in town, with their own storylines within Numenhalla, who provide quests. Preparation for a session usually involves designing one new quest a week (to replace the last one they took). Each dungeon section has a pre-built set of rumors and possible quests I use to help me.
Let's look at some of resources in the crypts. The Altar of Hierax can grant a long rest, The Anamneopolis allows speaking with the recently deceased. In the upper crypts, there is a pool along with a skull wall that whispers secrets. That's really what I'm talking about: What's still got juice in it after the players have extracted the treasure?
Then the restocking happens when you insert an antagonist for the quest. Note that this doesn't have to be a monster or new encounter. Perhaps some tunnels have collapsed, the resources is corrupted somehow or destroyed. The fact that the quest takes them somewhere they have been and the new obstacle/opponent exists makes the dungeon seem like a living place.
So preparation boils down to rolling on a combined quest table and inserting whatever idea is cool for an antagonist. I can manage one cool idea a week.
Setting up shopThis is the other problem. The players will meticulously map out an area and say, "Why don't we establish a beachhead here?"
The mega-dungeon represents the unknown dark into which we venture—the literal mythic underdark. You can't move into the mythical underdark!
Part of the greatest challenge of running a megadungeon is to keep the impression of it as a threatening unsafe place as the players grow in power, without robbing them of feeling empowered. We have many tools we can use to do this, cutting experience to the bone to slow player advancement, creating a threatening environment that kills players to remove experience gained from the players and more subtle methods such as scaling encounters based on party size and insuring that both overwhelmingly weak and overwhelming strong opponents are encountered.
But most importantly, Numenhalla is a time-locked dungeon. You can only enter it once a week, meaning moving in means surviving for a week. Can they? Even if I approached the problem as a neutral arbiter, I would consider it unlikely. There are worse things then I have listed on my encounter table.
But I'm not a neutral arbiter. I'm representing the chaotic unknown depths, the mystical underworld. As such, chaos abhors order and will react to attempts at colonization aggressively.