From Wiibrew:

The June 16th, or Version 3.3 update checks for and deletes Twilight Hack and any other Twilight Princess saves exploiting the same vulnerability. However, it does not do anything to existing Homebew Channel installations. It does, however, fix the Signing bug, which prevents any “trucha”-signed discs from running, including the Homebrew Channel installer ISO versions.

http://wiibrew.org/wiki/June16_update