Thanks for the suggestions I'll do so more digging on google and see if I can find any more info.
Things may not be as bad as I initially thought, as I was able to boot into workbench 3.9 off the HD after I booted into workbench 3.1 off of floppy.
@ AmigaMance - the reason the boot partition is on FFS is because I one 80GB hard drive partioned into two DH0:Workbench and DH1:Work. When I installed OS3.9, I isntalled OS3.1 onto DH0: using the standard install and hence FFS was the file system. I then installed OS3.9 and at that time I installed IDEFix97 and also SFS.
What I think I'm gonna do is copy everything off DH1: onto a USB pen drive - I've got 10GB of stuff to shift. I've already backed up DH0: onto a 128MB CF card, so I've got a copy of the OS.
I'll then wipe the drive and start afresh, but to stop this happeing again what can I do? I was thinking of using PFS instead of SFS or should I go with FFS with TD64? Any recommendations?