Polytron has announced that they won't be fixing the first Fez patch, and instead are re-releasing it as is despite the save file issue associated with it. The reason? Phil Fish states on the Polytron blog that it would cost "tens of thousands of dollars to re-certify the game." According the Giant Bomb, the exact cost for a patch is $40,000 based on a speech given by Phil at the Gamelab conference in Barcelona recently.
Phil adds on the blog posting that they "already owe Microsoft a LOT of money for the privilege of being on their platform." Polytron apparently has to pay Microsoft for being an exclusive on Xbox Live Arcade.
As for the patch, Phil states that it "fixes almost everything that's been wrong with the game since launch." Examples given were issues such as the framerate, loading, and death loops. "For 99% of people, it makes Fez a better game."
The patch was originally pulled as it would delete people's save file without notice. This issue apparently only plagues about 1% of players, and according to Microsoft the patch issue happens so rarely that it's considered "good enough."
Phil apologized to anyone that has or will be affected by the patch bug:
A truly shitty situation all around. There is some good news finally, as the Polytron Twitter just mentioned that the Xbox Live Arcade exclusivity will be up on "only a few months." Not much longer until the Steam release now.
WE’RE NOT GOING TO PATCH THE PATCH [Polytron]