I heard from somebody (David Rohl?) that the Labyrinth was probably an enormous administrative center, the bronze age equivalent of a cubicle farm, that Joseph built to handle the collection and distribution of grain during the seven good years and the seven years of famine. This was the main one, but two more were built at Thebes and in the eastern Nile delta; the city of Avaris (Rowarty) got its name from the latter one.
Don’t think of it as flooded—think of it as preserved for the Achrologists of the future
Thanks Berosus.