Aonuma says Hyrule Warriors isn’t a part of Zelda’s main timeline, set in a different universe
This information comes from Zelda producer Eiji Aonuma, speaking with Game Informer…
Within the Zelda canon, there is the timeline, but there has always been the sense of the main story and kind of a side story. Like, Majora’s Mask might be considered part of that, though it does exist as part of the timeline. With Hyrule Warriors, there is a link between the two, but it exists as a separate dimension, so it doesn’t exist as part of the main canon. Lately I have been thinking of it similar to The Avengers.
Maybe if you force it in somewhere, but that’s not something we want to do. The universe of Hyrule Warriors really is sort of a different universe and it is connected to the timeline of the Zelda series, but it is connected to several different games throughout the series. If you try and force this into it here [Aonuma places his hands in the air indicating different levels of the timeline], then…that information might not be complete. We really don’t want to put it in the timeline because it has links to the different parts of the timeline.