It was, but this is like hundreds (???) of years later, and there are whole societies up on the islands that barely remember prehistory.
You could argue that the few scattered towns and villages don't have any right to stand in the way of a renewed world. But like, a contrast to Ganondorf is another character from prehistory, who in the end blesses the game's protagonists with "This is your land!"
Reverting the world to its previous state would benefit no one living, and would destroy countless (tiny) societies and ways of life.
If you are unable to use this captcha for any reason, please contact us by email at email@example.com