Two Zelda timelines? Heaven forbid! (ancient spoiler alert)

[puffy]

That's called the split timeline theory and has been confirmed by Aonuma, the director of a whole list of Zelda titles and the producer of Skyward Sword: 

http://www.thehylia.com/index.php?subaction=showfull&id=1173298152&archive=&start_from=&ucat=19

Unless I'm missing something here..