"So the engineer has stated my change order request will not be approved. I am concerned about my liabilty in this issue due to not meeting the NEC. "
You can not install equipment that does not meet code regardless of the change order. I think its the engineers problem to solve and work out the problem with the owner.
"This project has turned very bad due to some other issues with design oh which I am taking a beating due to the engineer's faults."
You should not take a loss because of an error by the engineer. Had he got it right the first time you would have bid higher using the 600 kcm. He needs to step up and explain the facts to the owner.
