I would try to do it on PC.
IIRC, there is some software called 'Acronis true image', it should be able to clone it. just be very careful not to choose wrong device/partition of course..
If you have one of them Linux thingies, 'dd' might do.
On Amiga, you can simply partition it in same way and copy all files and directories. That way you'll also nicely defragment it. (there are CF adapters with slots for two cards-master/slave, but I'm not sure if they work fine on, say, A1200)
