When you do the things in the instruction above, until you get to the phase 4.) where is says:
"You should now have three partitions: /dev/sdX1 which is MyDocs, /dev/sdX2 which is MeeGo 1.2 Harmattan rootfs, and /dev/sdX3 which is the MeeGo 1.2 Harmattan home directory."

You will see the MALF file in your mounted Harmattan rootfs which probably will be something like /media/rootfs/var/malf if you are using Ubuntu. Some other Linux version might mount it to different place.

You can check it by command "ls -l /media/rootfs/var/malf", and if it exists, then you can remove it by command "sudo rm /media/rootfs/var/malf"