It is okay for me to remount cloop on compact flash after already mounted cloop from HDD, but how?
Just brainstorming: Maybe you can use the chroot and mount proc commands in the same way you would use them to do a Knoppix remaster when you copy the "Knoppix" folder to your hard disk and "chroot" into it to modify its contents: http://www.knoppix.net/wiki/Knoppix_...or_Remastering

However, I still think it would make more sense to run KNOPPIX off your hard disk with "tohd" and "fromhd" cheat codes.