The thing about Zelda games is that there is no solid history or lore, and the games are almost always only vaguely related (except in the cases of direct sequels such as Majora's Mask). It is implied that the skeleton knight is a Link from a previous generation. Which one specifically is completely irrelevant, and there certainly isn't any solid answer. As with pretty much all Zelda games there is no direct thought out correlation so much as a vaguely implied lore.
Zelda isn't a story based series. Miyamoto and his teams have always focused on making incredible gameplay, locations, and immersion and the story is an afterthought, merely something to add context to the actions. As such the series isn't tied together in the way Metal Gear or even Metroid is. All you have is a vague lore, and that's all it's meant to have.
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