What worked for me twice, once in a very similar situation, was to fill in the Missing Mileage Request form on the Web site and ask for credit for the itinerary as originally booked. After all, you upheld your end of the deal by showing up at the airport on time, tickets in hand and ready to fly.

You have to wait 15 days from your flight to send in the form or the computer bounces it right back.

Good luck!