I have modded a few consoles & always used gx loader i liked the gui more kiddy proof. However as time and system updates come along I started to get problems with gx. I am now using cfg with fat32 easier to load, easier to change settings it even tells you whats missing if you get a particular game error. I have seen some chat regarding a new version of gx. I would think you can either delete the gx channel in the wii settings. or uninstall the channel wad, you can then reinstall the wad you used before the update, then you should be back at the start. pre your gx update. The answers are all on this site you have to search and read lots before you act. never update anything without checking this site. your head aches may never go if you update at will.
Are you running a partitioned drive? Does your backup manager recognise the drive on your PC.