Nintendo Australia will fix your save file, if you send it to them.
http://www.nintendoworldreport.com/news/28727
Recently, it came to light that The Legend of Zelda: Skyward Sword contained a bug that could appear late in the game, which prevented players from continuing to its conclusion.
Nintendo Australia has announced their plans for how to have this issue fixed if you have been affected. There will eventually be two ways to have this issue resolved, but currently the only way is to ring Nintendo directly for details on how to send in your save file.
Nintendo is also preparing a program for those who have their Wii's connected to the internet, which will enable users to be able repair the save file from home. Details on the release and how to use this program will be announced on the Nintendo Australia website once they have a confirmed date of release.
Nintendo contact details for Australia & New Zealand are as follows.
Australia: (03) 9730 9822
New Zealand: 0800 743 056
[Hours of operation: 9:00am to 5:00pm Monday to Friday (Australian EST)]