If you ever run into this problem, all you need to do is start up an emulated environment using the encrypted ROM and then use a Kickstart grabber from within the emulation. As long as the drawer where you save the grabbed ROM file is accessible by the host system, you'll have yourself an unencrypted ROM.
Yeah, I figured that out eventually, but my A1200 has 3.1 ROMS so I even tried ripping them. They wouldn't work in the real Amiga, only in the PC with WINUAE, but it's OK now, I just needed to partition the CF card again with the limited MAX TRANSFER setting. Copied all the OS and files and games back over again and it was fine.
