First of all, you have to copy ALL the CD content to a folder, if you only want to modify the isolinux.
(This method only work if you ONLY want to change the boot/isolinux or the CD file content)

- Modify the file.
- Check that "KNOPPIX" file is in the <folder that you have copied the CD>/KNOPPIX/KNOPPIX (the last is the KNOPPIX archive)
- Create the ISO using

Code:
cd <folder that you have copied the CD>

mkisofs -pad -l -r -J -v -V "KNOPPIX" -no-emul-boot -boot-load-size 4 -boot-info-table -b boot/isolinux/isolinux.bin -c boot/isolinux/boot.cat -hide-rr-moved -o <folder where ISO will appear>/knoppix.iso  <folder that you have copied the CD>
Good Luck[/code]