ioFTPD may support FAT32 (note that I have never tried it) but ioBanana v20 surely doesn't. In fact, it uses NTFS streams to store important data such as race info.
Couldn't you move all other partitions to some real Linux filesystem while this one remains NTFS and then copy the data to another newly created partition ? You're not going to use ioFTPD while installing Linux, are you ?
