Never made sense why the timeline shifted here, now we see. This is the timeline created by zelda going back in time and bringing with her a secret stone. She has the full tri force because of the spell from the tragedy of princess zelda, and now the triforce is locked in her hand, which is how she uses it in botw. She creates the secret stones when she enters the past with a wish from the triforce, which is why the sages can seal ganondorf. the subsequent games never revive dorf, just calamity ganon, which is why all downfall games have pig ganon. 10k years later the sheikah make the divine beasts with technology from the zonai, but are later exiled because nobody trusts that zonai crap. The reason the secret stones are tears are because they are zelda's tears, and that's the tears of the kingdom, not the dragon tears, which are also zeldas tears while she used the triforce dragon to upgrade the mastersword to finally defeat ganondorf. It's also why she can transform back from a dragon.