It doesnt modify the game because that would be impossible, just the save file

Nintendo Japan has offered up a downloadable program to fix up your Skyward Sword save file if you get stuck with the game breaking glitch. The program is a new channel to download from the Wii Shopping Channel and its called the "Zelda Data Restoration Channel".

It works quite simply, you install the channel and it fixes the save file on your Wii, its almost patching on the Wii but not quite.

Nintendo Australia promised it would be offering a program to fix save files as well so expect this download to be made available worldwide soon. Much easier than sending your save file to Nintendo themselves. I did that to get a Mew on my Pokemon Red cartridge, that was back in 1999.

Source: Andriasang