I wouldn't necessarily say it does.
Kingdoms rise, kingdoms fall. Kingdoms get refounded. I believe that this Hyrule is a re-founding after the three timelines merge, which somehow destroys all of the old Hyrules. Because Ganon ultimately dies in each of the three timelines, he gets reborn as Ganondorf again in the merged timeline, and repeats the same song and dance he did in Ocarina of Time, only he's a lot more menacing this time because he's experienced life as a demon king in three previous timelines (how else would he just have been able to manifest Phantom Ganon without the magic powers granted to him by the Triforce of Power? The answer; he didn't, because he still had a fragment of Power in him from his previous lives).
The funny thing is, even if the old Hyrules were destroyed, their history lives on in not only legends and place names, but also the records of the Zora people because they just straight up mention Princess Ruto and her crush on the Hero of Time. The Goddess Hylia is mentioned by name in TotK, and the Goddess Statues all resemble the statue of Hylia from SS.
So, I don't think it's been contradicted at all, it's just that it all happened so long ago (not just 10,000, but possibly 20,000 or even 30,000 years ago) that hardly anyone remembers it as anything more than a myth.
Of course, at the end of the day, the timelines are really just a fun little thing to consider, there's not much that's too concrete about them. Wibbly-wobbly timey-wimey kinda things.
Alternatively, SS Link and Zelda didn't found the kingdom, they just founded the country-- the kingdom came much later. Rauru married a Hyrulean woman, after all, indicating that the land of Hyrule was called that long before it ever became a kingdom. Of course, that doesn't explain what Ganondorf is doing there, but still, it's something to consider.