Here is an alternate reason for the decline timeline.
When Link wins and is sent back as a child, this creates two distinct timelines, also two distinct realities. Sending Link back in time would not take him out of the adult timeline, as he would just grow up as normal, so the only other option is that it creates a rift, meaning that there are 2 new dimensions. When child Link is sealed in by the master sword, wakes as an adult, yet comes back as a child by placing the master sword back, this event creates a new third rift timeline in which adult Link doesn't defeat Ganon because he went back to his own time/dimension, and the world is left without a hero, much like the timeline where Ganon is defeated and Link is sent back. Without a hero to fight him, Ganon is victorious, he gets the other triforce pieces, I'm guessing when Link disappears, his piece remains behind, which after Ganon gets Zelda, he ultimately gets all three pieces, of course, his first wish when first touching and scattering the triforce could have been the cause of the dark world, when Link vanishes, the sages could trap him in along with the scattered pieces, meaning they aren't complete but are with him in the dark world leading to the decline timeline... When Link defeats Ganon in LTTP, he comes across the spirit of the triforce which brings the pieces together for him to touch(since they had been separated by Ganon's wish), which after his restorative wish should have scattered them again. As for Twinrova, I agree that she/they is/are resurrected. As for two more timelines since there are two oracle games, I feel this is unneeded since they both, no matter which you start with, end the same way(with Twinrova's sacrifice and Crazy Ganon defeated) besides the two differing timelines wouldn't even matter to the timeline of Hyrule as they both take place elsewhere.