Most people I've seen discussing the subject depict it as a Ben Kenobi moment; as Link goes into the Child Timeline, he disappears, but the MS simply doesn't go with him, so he just leaves the Master Sword, where it is then returned to the Temple of Time by Zelda.
I always saw it as just another timeline. When Link defeats Demise in the past, it creates a completely new timeline where Skyloft can descend down to the surface much earlier than it did during Skyward Sword. This is where I think Zelda U will be placed on the timeline, as the expansive...