(spoilers for tears of the kingdom!)
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so I've seen people discussing how Rauru and Sonia being the first king and queen retcons SS and going ways around it and kind of... disagree? there are other things I'd raise instead (like the lack of mention of Hylia despite how prevalent she was in BotW, but that's talk for another day) but I think there's a very easy way around it.
in the end of Skyward Sword, we see Link, Zelda and gang resettling on the surface. never in the game is it said that they founded Hyrule, though. (if it's mentioned in any of the books, good! I don't consider those canon.) it is very likely that they began settling this human community that came in contact with the Zonai and that eventually, several generations down the line, a descendant of Zelda (Sonia) married one of them, and together founded the kingdom of Hyrule, so Hylia's bloodline passed onto them.
