Well we can focus on the Child Timeline while referencing the other two at different points by the Sheikah tribe members and Impa who are tasked to help protect Link, Zelda, Arceus, and Blackfire from within the shadows. I have a headcanon that Impa and the Sheikah tribe are aware of the existance of two other Hyrules in different timelines. Now lets continue the story and how will we do Blackfire if she is alive? Captured maybe?