On the day of departure if a first class cabin is really empty the self service kiosks will offer upgrades for $45 up to $150 roughly. That should have confirmed him in first class and given him a seat assignment. Another type of upgrade would be a miles based one. $35 dollars for every 500 miles, but that only puts enough miles into your account to standby for an upgrade.
Either way, both of those are really easy to refund. Just look in the record, see that he wasn't boarded in first class, then refund the transaction. Sorry for your loss.
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