Well, for the catacombs at least it’s actually the other way around. As a TL;DR At the end of the 1700’s there were large sprawling networks of stone mines haphazardly placed under Paris that were threatening the structural integrity of the city, and at the same time the city was also facing a crises with graveyards literally overflowing. The Parisians of the time decided they could solve one issue with the other so they reinforced the mines and emptied the graveyards down below. Essentially they mined out the underground and filled it back in later with infrastructure.
The catacombs were cut as tunnels, mostly to harvest limestone.
Other than that. In the old days, it took a great deal of labor to haul stuff away. When old buildings were torn down (or fell down) and were repurposed, any usable material was scavenged for reuse, and the rest of the building would be mashed flat, filled in, and the new building built on top.
When an old city was left empty, because of a natural disaster or something, people forgot about it and didn’t go there anymore, because they didn’t have a system like google maps yet. Then, nature would take over. Plants would grow over it and fertilize the soil. Wind etc. would break down the walls and very slowly, a city becomes buried under layers of dirt, stones and plants. It is then invisible and people sometimes build on it without knowing it is there.
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