Another method of restocking dungeons is to use an idea from video games: radiant quests. I'm normally leery about the idea that one can simply port an idea over without much adaptation from one medium to another, but I think this is one of the rare exceptions. Once again, the idea is that restocking should be simpler than stocking a dungeon in the first place.
A radiant quest is one where there is a basic template for a task ("Go assassinate..." or "Go retrieve..."), and the game uses some mechanism to assign the object of that quest and the location it takes place randomly. In video games, radiant quests tend to be used to push the players to new areas (giving them a reward for exploring), but I think they work equally well for restocking areas of the dungeon they've already explored and cleared.
What you need is a bunch of generic tasks, a list of enemy forces and objects, a list of NPCs, a list of locations, and a list of rewards. I recommend starting with small lists for each one (d4 or d6 options) and expanding as new NPCs and new areas come up.
A sample generic task might run:
1) Retrieve something
2) Assassinate someone
3) Bring something/someone
4) Clear out somewhere
You pick one, or roll a d4 to determine what the basic structure is. Then you roll for the object or NPC from your lists of such to determine who they're supposed to rescue or assassinate or steal or set in place, etc. The list of enemy forces tells you what's guarding them. And finally, you roll from your list of sub-sections of the dungeon that the PCs have explored to determine where they're going to have to get to. Then roll to find out what their reward is.
This is all fairly simple. You can grab lists of enemy forces and treasure hoards from Red Tide, since this tends to be the most complicated part, or you can just come up with your own. You can even abstract this process if you have a bunch of mini-modules, and just randomly roll to determine where each module intrudes into the dungeon (perhaps with an earthquake or interdimensional portal opening to provide the explanation for the change).
The main things to vary are the task, the object of the task, and the location. Cycling through and recycling these in their various combinations can provide a fairly large amount of gameplay without much work (you can reuse forces and objects, and depending on how you handle it, this could either be lightly comic or build to a larger plot, as say, a particular magical artifact keeps on being stolen and returned to the dungeon in random locations, leading to the question of why it's so valuable and important).