This has gotten very confusing. Let's take it a bit at a time:

"He has not been repaid from the corporation."

He submits for the actuals, to be repaid by actuals. Otherwise, the company just gives him the allowable amount = "per diem." If the company hasn't paid him at all, there is nothing for the company to expense; they didn't incur it.

"I believe that the corporation can only deduct actual expenses because the corporation is not driving the truck"

You stated "owner operator" but you didn't specify "owner" of what?

Owner of shares in the S Corp, 10% or more?

Owner of the truck, which is not titled to the S Corp?

", the employee is and as a w2 employee"

"he can no longer deduct the expenses on Schedule A."

An employee was able to enter job-related expenses on Form 2106, and still might be able to in that State. But if you are not an employee, that would be self-employed on Schedule C. Your person is an employee for this corporation, so no Schedule C.