Find another routing. Do not "flatten" the wire to fit in some hole you already have. Seal the old hole, and find another way to get it to work. Damaging the wire at a bulkhead is generally not a good idea because of possibilities of shorting out.
To fit my runs of 0/1, I drilled holes in my floor, and grommeted the holes to prevent any rubbing or cutting from the vibration and movement while driving.
I believe this is one of those "little things" you have to do right. Hope this helps...