Note that this process is still ongoing. Often, when demolishing old buildings in dense (and expensive) cities, basements are simply filled, the whole ground is raised above the original ground floor, and ramps are added. It's just cheaper than digging the old structure out. Once all surrounding buildings go through this process, the whole road is higher than it was, and the original structure is "submerged".

Even when a road is repaved, the original layer is often not removed completely but the new road will still be laid down as thick as the original -- this is what happened where you see "sunken" drains or manholes (they will eventually be repositioned higher up when intolerably deep). In a few hundred years, again ground floors will have become basements. It's just how cities work.