The update system works on version numbers. It checked the IOS 50 and saw it had a higher number so skipped the updating of that file. Wiis are not supposed to go backwards in terms of system menu so the foolproofing isn't built into Nintendo updates.
Hope you do fix it but I can't see it being done through software. If you figure out a clever way to get into the NAND then I'd love to hear it.
Not really doing much Wii stuff these days.