Actually, TAs can process last-minute mileage upgrades (2 hours before departure), but oftentimes they prefer that you call your appropriate elite line to pull the inventory and have the miles deducted. That way it's already in the computer when the TAs pull up the PNR, and they won't have to call Customer Service to have the miles pulled and the certificate number inserted into the PNR.

It seems that what happened was that the computers went down while he was on the phone to the PLT desk. Thus, they were right to keep their original BPs and use them. Just call and have the mileage reinstated (if necessary).