It is speculated by some that alternate worlds such as the Twilight Realm and Termina may be unaffected by the timeline split. However, while these two realms are alternate dimensions, there is no evidence to support the idea that they exist outside of linear time. Both realms have demonstrated the ability to receive beings from the Child Timeline and return them to the Child Timeline when they exit back into Hyrule. There is no reason to believe that these two realms would only exist as a single timeline, or that they could "prioritize" inputs from one timeline, and later output these into both the timelines.
In addition, the renowned Youtube show, Game Theory, dismissed the Zelda Timeline, particularly the Defeat Timeline (in where Link fails on his quest) on the grounds that "the hero cannot be simultaneously victorious and defeated". Elaborating, he explained that with Link defeating Gannondorf, two perfectly possible timelines are created; However if Link dies at any point in his journey another separate timeline is created. Explaining that the only way for all 3 timelines to exist is the Many Worlds Theory (the theory that all possible pasts and futures exist in separate timelines).