That would be a very interesting thing given that he doesn't have that passport on him, but it really makes no difference how things were entered into the computer. He just has to explain his situation when he gets to an officer and they will take care of him from there. This will not be the first time they will have encountered such a situation.

That he has a copy of his US Passport might be helpful to CBP, but isn't necessary. If the line for the primary passport control booths is long and your son can spot a roving CBP officer, he might want to walk up to that officer and explain the situation. That officer might walk him right to immigration secondary letting him skip the line for primary.