I was confused for a long time, and I've gotta say this:
My theory is that Link was sent before the Door of Time was actually opened yet after Link is already at Hyrule Castle. My theory states that the Triforce of Courage opened the Door of Time to let Link through, then resealed it.
Now, let's say my theory is correct, there are numerous things that would have still happened and others that would not have happened.
Happen:
1) Great Deku Tree is still dead.
2) Saria gave Link the Fairy Ocarina, yet had not taught him Saria's Song.
3) Link most likely will meet Malon and definitely meets Zelda.
Doesn't:
1) Link did not meet Darunia, Ruto, or Nabooru.
a) Link and Darunia did not become "Sworn Brothers".
b) Link and Ruto did not become engaged. Thank you Nintendo!!!!
c) Nabooru isn't captured by Twinrova.
d) A and B are still possible to occur, but we can't be sure.
2) When Zelda sent Link into the past, he most likely lost his unequipped items. Things like the Bomb Bag, Goron's Bracelet, Fairy Bow, etc. This explains why Link doesn't have them as he goes into Termina. Also, he may have lost his Fairy Slingshot and Fairy Ocarina during the year he was in Hyrule. It makes sense, they're small.
Questions:
1) What did Link's presence change? How is it that King Daphnes trusted Link, a stranger, yet not Zelda, his own daughter?
2) Had Ganondorf already resurrected the Dodongos and cursed Lord Jabu-Jabu?
3) What did the "Hero's Bow" of the Gorons come from? Is it the one from
MM?
4) In Termina, there is the Hero's Bow, a legendary weapon used by a Hero. So, if this Hero isn't Link, then who was it? Was the Fierce Deity the Hero who used this bow?
5) Wasn't Zelda's prophecy made impossible when Link was sent to the past? After all, he didn't have Navi, he didn't stop Ganondorf himself, etc. Thus, the prophecy would have to be fulfilled later on by another hero, but apparently not
TP Link. He doesn't have a fairy or a pretty, green stone.
6) Unimportant, but how did Link convince Malon to lend him Epona when he left for Navi?
If anybody's got answers to my oddball questions, please fill me in. If not, then oh well.