You can safely run through the whole guide again, though I wouldn't recommend deleting the homebrew channel and I am positive it wouldn't help. It sounds as though something became corrupted on the SD Card at a hardware or firmware level. First thing to check is that the card is in regular mode, not write protected. This can be done on most SD Cards and adapters by flicking the small switch on the left side of the card. Next up try FAT16 instead of 32, see if anything will read. You may run into some limitations imposed by the file system though, not sure, so if you get something to read in FAT16, try FAT32 again. Next up make sure your apps are all set to read homebrew apps off the SD while that card is plugged in. Doubt that's be an issue but we might as well cover the bases. Other than that idk. There may not be much that can be done.
@Kafluke @Robins any ideas?
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I believe IOS58 is a valid choice and should work just as well as a cIOS in most cases. I would let it stay on IOS58 if the cIOS are having issues.