k so all people here who wonder where zelda twilight princess comes into the timeline and your a splittist (believe in a split timeline) i think i have the answer. twilight goes into hyrule B (the one with zelda but no true link) and before windwaker. ganon himself splits too. so the twilight world is a shadow of hyrule b (a.k.a hyrule a) and vice versa. when you get to forest grove with the master sword and enter the temple of time, in hyrule b it is destroyed, so in order to play it you need to have the door that transports you to a mirror of hyrule a.
i have more but so far my fingers are tired. what are your theories in the timeline of zelda?