.
To stack permanent serial compressed image upgrades to KNOPPIX, use the magic incantation,
assuming KNOPPIX1 was the previous upgrade:

cd /
sudo mkisofs -R -U KNOPPIX-DATA | create_compressed_fs -B 131072 -m - - > /mnt-system/\
KNOPPIX/KNOPPIX2

(Sorry this line a little too long for this forum, so used the '\' sign to show it here.)

Then reboot to see if it all works like it did in the previous persistence file.
If so, move knoppix-data.img from /mnt-system/KNOPPIX/ to /mnt-system/ temporarily and reboot.
Re-establish persistence and again verify that KNOPPIX2 is doing what if ought.
When you are really sure KNOPPIX2 and persistence are ok, remove knoppix-data.img.

Dont count on PCManFM to remove things; use root and rm to do this.
init's mountunion() looks like you may have up to ten such upgrades, if you have enough space
on your LiveUSB