Orici and Aeffles have summed it up pretty well.
You go back to before you ever touched the Master Sword, so Ganondorf never gets the Triforce.
OoT Adult Ganon[dorf] is sealed away
OoT Child Ganondorf is still plotting how to get in the Sacred Realm

The most likely scenario for Link is that he essentially 'becomes' the Link from the Child Side.

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Bomber's Notebook | Zelda Informer, Home of The Bombers | Theorizing Resources | Aralith's OoT Retelling
Voted as Best Zelda Theorist in the Summer '08 Awards. Thank you to all who voted, and to all who inspired me along the way!