Story Notes:
Most of what follows is sheer speculation. The point I am trying to get across is that, though it does appear that a timeline split occurs at the end of Ocarina of Time, Link gets sent back, and the future world is destroyed.
This is an article basically just to explain my interpretation of the ending of Ocarina of Time. It is a good idea to refer to this video when reading this article.
There is some dispute as to what happened after Link was sent back in time by Zelda. Link awakens in the Temple of Time and immeadiately rushes off to warn Zelda of the events to come. Link is the only one who knows about the events to come, like the Imprisoning War, and the murder of the King by Ganondorf. Zelda, as indicated earlier in the game, had been having dreams about a light shining forth from the forest, and so she believed what Link had told her about what was to come. She then went and told her father all that Link had told her. The King of Hyrule knew of Zelda's magical ability to see the future in dreams, so he believed every word she said.
NOTE: Link wakes up before any of the events in the Temple of Time occured, so the Imprisoning War had not yet happened, and no one knew that Ganondorf was the King of Evil. He did wake up, however, after Ganondorf had gone around asking for the Spiritual Stones [for proof, watch the ending scene of the game: it shows the new Great Deku Tree because the old one had died due to Ganondorf's curse].
The King secretly assembled the seven sages, and told them who they were. He then asked them for their help in sealing Ganondorf away. They do not, however, want to seal Ganondorf away in the Sacred Realm, for he has not yet (in this time) touched the Triforce. The sages reveal to the King the story of the Twili, the ancient race that had been sealed away by the gods in the Twilight Realm. They then decide to seal Ganondorf into the Twilight Realm.
The sages then replaced the Master Sword and scatter the Spiritual Stones over Hyrule. Link spends what is left of his life with the Royal Family in Hyrule Castle, with only the sages, the Knights of Hyrule, and the Royal Family knowing what Link had done to save the Land of Hyrule.
