Here´s the simple version:
Most of the ocean's bottom is oceanic crust composed by basalts; its almost 3km below the sea's surface, in average. Maximum global sea levels changes are around + 500m in relation to the present sea level (we have a pretty good track of this along the Phanerozoic thanks to the oil industry). This means most of the oceans' bottoms have never been exposed above sea level; actually these areas have nerver been even close to the maximum sun light penetration depth.
Continental crust, on the other hand, is composed by less dense rocks such as granites, covered by a thin veneer of sedimentary rocks. Vast inland seas like the one which once covered lots of North America back when dinosaurs ruled the Earth were shallow seas (no, its not the case of the Mediterranean sea) whose bottoms were composed by continental crust. These probably were the seas where the fossil seashells at you backyard lived. They were most likely created by a combination of elevated global sea level and relatively small and slow continental crust subsidence during sedimentary basin formation.
In sum, the geologic records do not show any vertical movements large enough to bring a large area composed of oceanic crust above sea level (small slices may be smashed and uplifed where tectonic plates collide) or to bring down (and later up) large chuncks of continental crust down to the same level of the oceans' bottom. No, that's not what subduction does.
And by the way, we have pretty good maps of the oceans' bottoms by now. We know the topography and geology. OK, its not in the same level of detail we know the continents, but the major features are known. But guess what? Nothing which could be related to Atlantis, Mu, Lemuria, Hyperboria, etc. has ever been found. Nothing which could be related to the infrastructure an underwater technological civilization would require has ever been found too.
