Can I just check. If I install the standard OS3.9 install is there any risk of me damaging the Roms in my CD32?
No. It's just a patch that is loaded in RAM. If it borks your system, power it off for long enough to completely clear the ram (~30 seconds) and power it back up. Back to normal. Not that I've ever added a wrong ROM patch to a system.... No, not at all. (innocently whistles)