I mean how exactly do you acknowledge another timeline in-game?
I think twilight princess might be the best instance of this though, it's a sequel to ocarina of time's child ending, but it came out after wind waker, which was a sequel to the adult ending, so they definitely made the game knowing that it's on the opposite side of wind waker's canon
Make it a story element. You could allude to Ganon, Link, and Zelda remembering things that haven't happened. Lives they haven't lived. Maybe aspects of other stories start to bleed over.