Along with PFS3 comes a tool in the PFS tools directory called PFSDoctor. Use it to fix your drive. It's fixed what few problems I've had with mine. If for some reason that fails, there's also DiskValid in the tools directory. Just type DiskValid FIX and everything should be back to normal. You might want to read up on the DiskValid command just to make sure you're familiar with it first though.
Another thing I'd suggest is, if you're working with a SCSI drive, make absolutely sure your termination is correct. The last time I've had drive problems was a long time ago, before I knew anything about SCSI. I didn't check close enough to make sure my chain was installed properly and I'd get drive errors with some frequency. Once I got that all straightened out I haven't had a drive problem since.