When it comes to formation of soil, the equation is pretty daunting. About 1 cm for every 200 years in a tropical environment.
Given that you want to cover 65 meter buildings with soil at a height of 1 meter, the amount of time would be the number of centimeters times 200 years.
6600 cm x 200 years= 1,320,000 years
That's a lot of time.
As to Subsidence, that's going to depend greatly on the ground you build it on, and quite honestly, no one is going to want to build atop a region that unstable. I live in a place where this can happen. Believe me when I say that no one is looking to build on top of the sunken building, because they know it's unstable. It's often a result of limestone, karst topography and a shifting water table.
Yes, buildings can unevenly sink sometimes as much as 1 meter a year, but generally they reach a tipping point, where they either stabilize or--half the house falls into the newly formed sink hole. Generally they do not uniformly "sink." That seems to be what you are picturing but it rarely happens this way, and would be strange indeed. There are measurements of places where they have said like "sinking at 2 feet a a year" or something, but you have to realize that is the AVERAGE. There are always places where it's more or less, and it's hell on a building when the left side is 1 foot higher than a the right.
I cannot give you an equation for this one because rates of subsidence vary widely, from place to place and soil condition to soil condition.
If the buildings are in use, folks may clear things away, or strengthen foundations.
It's a better idea to have a sudden disaster hide buildings under rubble that was then used as a foundation. Or-- your city dwellers can deliberately build at a higher grade for plumbing like Seattle! Check out their underground buildings!
If a ruler or society decides that they want to rebuild at a certain level, they can preserve the lower levels, sometimes because the original owners complain, sometimes because they want room for sewers, do not underestimate the power of public works systems.Some can just be closed off when building another section and forgotten--there are abandoned subway platforms like this.
The issue with natural covering up of dungeons rather than conscious building is that in-fill is more likely to happen. It's not...like a lot of fun for people to dig out an old city, but it is fun for them to explore it. The only way that can happen is if people actually build over it.