This is a rough sketch, I'll try to come with more detail soon. I have a feeling the submerge of Atlantis could also refer to the shaman's descent (perhaps through the underworld/netherworld) or a release of past outdated energy (biologically speaking trauma). Such an outburst could lead to similar destruction both within and without.
Similar to the story of Yu who then had to pace/dance the steps to rebuild what the flood has destroyed. Alchemically speaking it would most likely refer to excess water clogging the dan tiens.