One big problem:
If the timeline actually does split as the maker of this thread suggests, then the Princess technically wouldn't know there's two Links.
If the split occurs because two Links can't be in the same timeline, then that means Hero Link warns Zelda and goes off to Termina.
But since there's a split, Reject Link goes to Zelda, and the whole game of OoT would happen over again.

If there are two Link's co-existing, you need to explain how the timeline works with two Links.

If there are not two Links, because the timeline split to separate them, then in the 'reject' timeline, Hero Link never returned and warned Zelda, and thus Reject Link would be the first Link to talk to her, and OoT would happen all over again.

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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!