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Have you tried wbfs2fat.py ? It might help to convert to fat32 and see if it fixes SOME problems. There's also a recovery mode of sorts in Wii Backup Manager that you might try.
I had the "if it aint broke" mentality until yesterdays drama.
Never had a single issue with WBFS until yesterday.
Reading around, it seems I should cut my losses and obtain those games again somehow.