The time scales in Golarion are ludicrously long. I have myself complained about it in public on a couple of occasions. There was a lich in Book 5 of Ruins of Azlant who had 10,000 years to accomplish his clearly defined goals. He had daily access to high level wizard magic and reliable prophecy, and yet somehow in that time he managed to accomplish approximately nothing. He conquered the twenty miles of terrain surrounding his tower. Woo. Ten thousand years, and he got about as much done as one mundane tribe of barbarians could do in a summer.

So believe me, yes, I'm well aware that logically this city should be nothing but a large mound. But certain aspects of the overall plan for the campaign mean that I have to retain compatibility with the established canon lore. I'm stuck with the stupidly long timeline. And the plot demands a more or less intact city. I am therefore ignoring the fact that this place should be a nice big hill. In the event that a player wonders about it, I shall wibble gloriously about ancient protective magics that have warded off wind and weather and time to an astonishing degree. Truly, the ancient wizards of the Shory were astounding, blah blah blah blah.

Ultimately, I'd like the PCs to have the option of reactivating the aeromantic infandibulum and flying the city home in triumph. So making them excavate the entire place wouldn't really work, I'm afraid.

I'm definitely going to add damage and overgrowth. I just need to figure out how to do that. Preferably without having manually adjust all 2,495 buildings. I'll keep fiddling with it.