Perhaps try creating an emergency boot disc with OS3.9, then install the OS. Once that's done you can create/edit partition table and file system used. Use a 2nd partition, then copy the OS files across to that, use boot menu to select the secondary OS install, then partition/format original OS install partition with pfs, then copy back. This last step is only necessary if you want the boot partition to also use PFS (recommended anyway).
There's a bunch of ways to go about it, but this should work.
edit: if you find yourself having problems booting the OS3.9 disc (sounds like your current install may not be stable enough) then Winuae might come in handy as you can boot from an ISO without the need for cd drivers. Once its installed you'll have access to os3.9 hdtoolbox and you'll also be able to update your file systems with whatever you like, so you can complete the process on your amiga (or do it under winuae, the choice is yours

Good luck and feel free to ask if you find yourself stuck again.