Last Year I had a similar problem, I misplaced my & my wifes BA boarding pass from Barbardos to London Gatwick in J class.

The process is simple to recover the miles, you need something called a 'Travel Certificate.' What this is, is that you have to enquire with the airline where to send this enquiry, and write them a letter asking for a travel certificate.

Note to them the date, start and destination of the flight, flight number, and other details (such as what class you were in). They should write back to you with an official letter (this is the flight certificate), confirming your name, and details of your flight.

Once you have this, pass this on to your milleage program, and they shouldn't have any problems crediting your miles.