HUGE EDIT: I deleted my previous post to completely change my idea:
The is no split. My ideas are insanely similar to that of the Butterfly effect. Link's Childhood spirit is trapped in the Sacred Realm for 7 years. When he drops the Master Sword back in the Temple of Time, his spirit controls the child body that was left behind. This way, child Link is still being controlled while his spirit is sealed away. At the end of the game, Link closes the Door of Time and travels to Termina. After these events in Termina, I believe he goes back to the Temple of Time and resumes events after he defeated Ganon.
"Whenever there is a meeting, a parting is sure to follow. However, that parting need not last forever... Whether a parting be forever or merely for a short time... That is up to you." -Happy Mask Salesman
Anything I post about the development of a new game should be regarded as a game that I am making unless stated otherwise.