Actually the "chunk" that is missing from the right hand side of the
disk is what allows the computer to write information to the disk. So
to format the back side of the disk, in a standard Apple II drive,
you'll need to cut a similar notch in the left hand side of the disk
directly across from the notch on the right hand side. After you've
done that you need to turn the disk over and put it in the drive to
format the back side. Also using MacADT or ADTPro to copy the disk
images to the disk you'll need to turn the disk over to write
information to the back side.
In fact if you've been trying to write the back side of the disk
without first notching the left hand side and then turning it over
it's possible that you been writing over the boot side of the disk
every time.
Just my two cents worth,