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sounds like you just said you were able to get an empty folder to work...???it is not red anymore, if i re-calculate them in wii backup manager, the red text dissapears, and they all do work, but it will only make four folders with content. the rest is just empty. they have the right name, so can i just copy the isos, into those folders?
i do not know where the problem is comming from
Chances are pretty good that the images (ie. ISOs) you have are corrupted and that's why WBM isn't copying\converting them over. You can't just copy the ISO because your FAT32 HDD will not permit you to copy files greater than 4GB to it.
You can test the ISOs in ISO form on an NTFS hard drive, but I'm willing to bet that it will fail because I think the game image itself is corrupt.
You can try using another backup manager to transfer\convert the game to wbfs. I think wiimm's tools might even have a cmd line function to verify the integrity of an image, but it definitely will have a command to convert ISOs to WBFS files. Other wii game transferring\converting apps include Wii Game Manager (kinda outdated), spayrosam's new "beta" app, etc.
all in all, I think you might just have to accept that some of your backups are corrupted, and the originals were eaten by your dog. If you can't handle that disappointment, then you might be forced to go buy the same games again (or resort to piracy, but plz don't do that)