The summoning order issued by the Imperial Court wasn't for building a new city, but for cleaning up a city that had once been submerged by floodwaters.
Compared to constructing a new city from scratch, cleaning up a city that had been underwater can save a lot of building materials. Although those buildings had sunk beneath the water for several years, as the saying goes, "Some things can endure a thousand years dry, ten thousand years wet, but not half a year both." It was like the dragon boats in Cantonshire. The best way to preserve them was to sink them to the bottom of the river and salvage them when needed.
Moreover, those shipwrecks at the bottom of the sea, even after hundreds of years, still maintain their rough outlines under water.