Don't forget the idea of a city silted over or sunk into the ground due to some natural calamity or another. As time moves on people will tunnel down into the area looking for treasure, animals will begin to lair there, more animals will come to hunt the ones living there. Areas would be taken over by either humans or some monstrous race. Think of the salt mines near Wieliczka, Krakow that are over eight hundred years old and places people have not visited in hundreds of years. Or the big cavern system near Porta Rosa in Slovenia. Then add in the fact D&D has all of the underground races which natively are already living far under the ground. Take a page from Florida and have a few houses fall into a sinkhole created by Derro years ago....