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(please understand i don't know everything about these games)
seeing conversations about tears of the kingdom on if zelda had stayed a dragon the prophecy would've gotten fucked afterwards, but like... what about before? if she's been an immortal dragon then what about all the other zeldas? sure that can be explained away through time travel bullshit but what about dehydrated ganondorf? he's been alive under the castle the whole time, shouldn't that have fucked with the prophecy as well?
this is why i choose to believe that either:
those two just kinda got kicked out of the prophecy due to their circumstances
or
botw/totk are in a completely different timeline than skyward sword and everything after that. no demise. no prophecy. sure the triforce still exists but ehh it's role in a lot of games has always been minor(not saying in all of them mind you) including botw/totk
edit, the second theory also explains why there's both zora and rito at the same time in the ancient past