I think that's the idea Nintendo was trying to give us with Wind Waker and Ocarina of Time.
I always thought that it was just like the guy above me stated it as. In OoT, there are literally two different worlds: one where the mastersword hasn't unlocked the gateway to the Triforce, and the one where Link pulled the sword and allowed Ganon to gnab the Triforce.
And as we all know, once we banish Ganon in OoT, the Princess Zelda tells us her mistake and promptly returns us to our childhood where we belong. The land of Hyrule is safe (both in the present and in the future).
What cannot be is the idea that Link somehow scattered the Triforce of Courage before leaving for Termina, nor did it shatter because he left. The childhood timeline has no impact on the world Link left behind (the one where he banished Ganon). So what must have happened is when he left the world 7 years in the future for the last time, the Triforce must have been hidden so a repeat of the events couldn't occur.
This Hyrule that was saved by Link represents the main timeline because it perpetuates the Legend of the Hero. The timeline that leads to Majora's mask will do something totally unpredictable and unrelated to the Legend of Zelda most likely.
So, Ganon is locked away with his evil power, which begins to build and grow. He never actually breaks free of the seal, but his evil power is spilling out on Hyrule. When the Hero doesn't return, the gods or goddesses flood Hyrule to cover up the evil. With time, Ganon is able to cause the forces of good, and the new Link, to seek after the mastersword, which then frees Ganon of the seal that was keeping him locked away. Ganon then immediately goes after the pieces of the Triforce that are hidden away.
My best guess is that when Link is returned to his childhood for the final time the Triforce of Courage is split up and hidden across the land to help prevent this thing from happening again. It took the new Link to repeat past mistakes for Ganon to have a shot at obtaining the Triforce.