“Mysteries are still around us when it comes to the Zelda universe. While Hyrule Historia gives a logical and (more or less) solid timeline that places each game in its correct order, it fails to provide further details on in-game events, let alone what happens off-screen, such as backstories and events between games to tie them in. As awesome as the book is, it’s far from being a complete encyclopedia.”
Johnathan Vega of the site Zelda Informer has published an article exploring what exactly the ‘Divine Prank’ the Sages of Twilight Princess are referring to, and the ways in which it would be possible. Overall, it looks like we have a gap in our timeline!