I could be barking up the wrong tree entirely, but did you update the OS on the primary drive from a FAT32 file system to NTFS, i.e. did you upgrade from Win9x or ME to W2K or XP? Not sure if that would be a reason, but perhaps it's just not 'seeing' the data on the second drive, rather than it having been deleted somehow.
As I said, that could be totally wrong, so best wait for a proper techie to reply, which should be soon.