Zeal is actually based off of commonly shared mythology between Aztecs, Japanese, etc. They talk of an advanced civilization (presumably technologically advanced... or in a way better than our current civilization) that was lost during the ice age, presumably from the ice melting and it sinking beneath the ocean. The Japanese version of the myth said it was a floating civilization, and hence, Chrono Trigger is Japanese-made. Though, if it flew, but was lost, it was lost due to massive condensation in the clouds. Clouds gather water, and after the ice age, they gathered so much water, it rained heavily and this civilization plummeted to earth because of the heavy rainfall.
This is just my theory though. As it is, explorers have discovered highly advanced ancient ruins off the coast of Japan, which could be a possible link. Also, remember that humanity has only explored 10% of the entire oceans on the planet. We know our own moon better than we do our oceans. Not to mention the Bermuda triangle could hold a possible key. My idea is possibly if there was such a civilization, it probably crashed there and left an effect on the body of water there. Everything that enters the triangle never returns. Even planes from WWII were discovered to have sunk to the ocean floor there.