You could hook the drive up to your PC, run winUAE and copy your files you need to keep to another drive on the PC, then just wipe the drive, re-partition and then re-load WB then copy your important files back to the drive.
I just had a drive go bad and had to hook up a spare to my PC and basically do just what I described. The drive booted right up when I put it back in my 4000, only thing is after all that the mouse craped out on me.
