Everyone except for Rauru is stuck as girls, but it's better than being bimbos.

Sadly, even with the combined magical know-how of Sheik, Rauru, and Impa, there was to be no cure for those whose gender had changed. Sheik, Link, and the entire population of Kakariko Village were now women. Sheik didn't seem to care much, for reasons she kept to herself. Link decided to take the name Linkle, and while she clearly missed her original gender, she adjusted with time. Linkle continued her quest and defeated Ganon, even doing a happy dance on the spot afterwords. When Zelda, who had been Sheik all along, offered to send Linkle back in time to before this entire mess, putting her gender right in the process, Linkle surprised everyone, including herself, when she decided to sleep on the question.

The entire population of Kakariko, effectively the remaining Hylian population of Hyrule itself, left for more masculine pastures. Even those who didn't want to be dating men now, few that they were, couldn't support themselves in the wasteland that remained of Hyrule. Eventually the Hylians found a nearby people who they intermarried with, and with time they adopted the Hylian system of government and the Hylian Royal Family.

Linkle kept putting off her decision, until the day she met Lin. After a whirlwind romance, Zelda received a letter telling her that she wouldn't be needing that time-travel spell, as well as the invitation to a wedding.

THE END

...or is it?