I'm fairly certain that OoT Link does not exist anymore in the Adult Timeline after the end of OoT since he is definitely sent back in time by Zelda at the end. I'd rather trust the words of the actual games and Hyrule Historia than the Encyclopaedia which I know is wrong for sure on certain parts.
Anyway, if we ever want a game depicting the Great Flood, then the protagonist cannot be any version of Link, nor any other hero character, seeing as we learn in WW that the reason why the Golden Goddesses decided to flood Hyrule in the first place was because no hero arrived when the kingdom needed someone to save Hyrule. I've wanted a game about the Great Flood for a long time, but it would inevitably have to be at least somewhat of a tragedy, with a protagonist who fails quite miserably. That's my take on it anyway.