Actually, on the 'RVL-RZDE-0A-2' version of Twilight Princess, the codes do only work on Ocarina, and not any of the GeckoOS versions with Ocarina support. The 'Must Be On for Zelda TP v2 USA [James0x57]' code becomes corrupted. However, you can convert Ocarina into a DOL file by using the following tool...
Super Simple Elf2Dol converter for Hombrew Channel beta9The above tool will make it usable on the Beta 9 version of the Homebrew Channel.
Also, you should be able to start new game files on the empty slots, and not break the Twilight Hack. You just can't move the Twilight Hack slot.