I've got a dual boot machine. Windows XP on the C Drive, Windows 98 SE on the D Drive. These are two physical hard drives. Both are formatted FAT32. The only files used by Windows 98SE on the C Drive are the boot files; everything else is on D.
If I change the C drive to NTFS, I know that Windows 98 will no longer be able to see it. I'm fine with that - I just want to know if in the initial boot stages that will cause a problem for my Windows 98 installation.