The answer there is that it’s the academics who don’t realize the original city is there; the people who live there usually know there’s more city underneath.
This can come about in a number of ways: in Venice, when the water level rises, they build a new level on the top of the buildings and shore up the old basements, often by filling them with rubble of the places that didn’t withstand the pressures of increased height.
In places like Jerusalem, it’s due to conquest. When a new group invades and tears down the walls, the old foundations are left, and the dirt of daily life and rubble makes it easier to build on top than to re-excavate.
In other cases, the city is abandoned, and nature does the rest, blowing in sand and dirt. But cities are usually built in the first place because they’re at an advantageous location, either along trade routes or water access points. So eventually someone is bound to come along and decide to rebuild.
In most situations, what is buried is only the foundations of buildings, not entire structures.
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