I predict that the Zonai are the descendants of the people who remained in the sky.
Skyloftians evolved down two paths - The Oocca and the Zonai.
The Zonai structures seem to be the ones that are in the sky exclusively.
Perhaps all these Zonai structures fell to the surface, they assisted the Hylians in sealing away Ganon, and lived on the surface. Their sky islands and structures eventually sank deeper into the ground, sediment and rain over eons shifting the ground and burying these islands; making them indistinguishable from the typical landscape.
However, the breaching of Ganon's seal has caused these islands to awaken and rise into the sky.
And Link must collect the seven Tears in order to re-seal Ganon and cure his Calamity that is plaguing Hyrule once again.