I used this command to rebuild the 'iso'

#!/bin/bash
mkisofs -pad -l -r -J -v -V "KNOPPIX" -b \
boot/isolinux/isolinux.bin -c \
boot/isolinux/boot.cat -no-emul-boot \
-boot-load-size 4 -boot-info-table -hide-rr-moved \
-o knx/nick.iso files

where 'files' was the directory containing the unzipped files plus all the files and directories copied from the original CD.