According to developer Polytron, the game would cost too much money to recertify.
'Fez' was an industry darling for years before it was released, and made a huge splash when it launched. Since then though, the game has had some issues. One of the biggest of these is a patch that straight out deletes the saves of some players who have completed the game.
"Microsoft would charge us tens of thousands of dollars to re-certify the game," says Polytron. Because of this, the patch that initially went into effect – the one that deletes saves – is coming back online. Polytron assures that "the current patch is safe for an overwhelming majority of players."
Source: Game Informer