Thats exactly what I was thinking. Good movie, btwSo if all of what happened had happened, and then Link is sent back in time after defeating Ganon, wouldn't there be two Link's in the past? One that is in Kokiri Forest and just beating the Deku Tree, while the other is the Link you play as who was just sent back in time. If you've seen the movie, Back to the Future, you'd understand a bit where I'm coming from with this angle of looking at it.
I don't think we'll ever really know what was going on, unless Nintendo releases some kind of official timeline for the Zelda series.