"Content in Hyrule Historia isn't canon because I said so! We shouldn't take Ganondorf's statement at face value despite me having no way to substantiate that! Even though reincarnation is a magical concept, people can't reincarnate in one timeline if they move to another timeline because I said so! Demise can't be reincarnated because his body was sealed inside a sword and because it doesn't work with how I arbitrarily define reincarnation and also despite Aonuma specifically confirming that he's Ganon's origin!"
That's what I got out of your post. Honestly it's pretty clear to me that you're just moving the goalposts here and completely disregarding or reinterpreting things that are inconvenient for your argument.
The only time two Links actually coexisted was in Twilight Princess, and that was A) in some other realm which could have been Link's mind for all we know, and B) a game where one Link was a blood descendant of the other anyway.
Hyrule Historia does not present the manga as canon, just as a bonus. The manga is created by the same group that made mangas for every Zelda game and none of them are canon. They are very loosely based on the source material and deviate wildly from the games. The Skyward Sword manga is no different and is full of inconsistencies with Skyward Sword. The biggest one being that the Master Sword is in the manga despite it, you know, not existing until it is created in Skyward Sword.
If the spirit that is being reincarnated is completely removed from existence how can it reincarnate? If this is not a problem why does the flood happen in the first place? Was the Hero of Time just being a dick? Why does the analysis of the gods and King of Hyrule not matter? Everyone else says he's not related to the Hero of Time.
To reincarnate obviously a spirit needs to be available to do so. Reincarnating is to take flesh again. Seals are made to trap spirits and prevent this from happening. Seals have to be broken for this to happen in all the games where a sealed spirit reincarnates. Furthermore, Demise does not say HE will reincarnate. He says that an
incarnation of his
hatred will exist throughout time. Thus SS explains Ganondorf as fulfillment of this curse, as Ganondorf is even more full of hate than Demise was.
Adventure of Link: Generations of Princess Zeldas exist while one sleeps.
Twilight Princess: Double Link action.
Spirit Tracks: Zelda prays to Tetra and Tetra answers the prayers.
BotW: Hylia talks to you and blesses you via goddess statues. Also Zelda's mom and supposedly every female born in the royal family had the goddess powers.