Why convert to .iso to have wiiflow try to read it? USB loaders are designed to read .wbfs files.
Have you checked our FAT32 or NTFS guides that show how to set up your hard drive and methods of properly installing games to it? (links to both are in my signature)
When I went from WBFS formatting to FAT32 formatting, I used WBFS manager to convert all the games on the hard drive to .iso files, then used Wii Backup Manager to reinstall them to the newly formatted drive from there. Not all of them worked. I had to delete the resulting .wbfs file and rerip it off of the original game disk again to create a good one. You may have to rerip your games as well if this is something similar.