I'm very confused ? Are you refering to this:
Does Magic Lantern completely replace Canon firmware?
No. Magic Lantern runs from the card, as an add-on over standard firmware. You will still be
able to access all Canon functionality.
To go back to Canon firmware, you may:
• Press and hold SET at startup to bypass ML only once (for the current session).
• Format your card in the camera and choose to remove Magic Lantern.
• Disable the bootflag (this will uninstall ML from the camera; to do this, run Firmware
Upgrade and follow the instructions).
I does not work for me and I have tested several times and if I run the firmware update again it does not remove the bootflag, I get a msg that says that the bootflag is set everytime. And I dont get the question if I want to remove ML when formatting the card