Does your boarding pass stub have your BA number printed out on it? If not, there should be no problem, as long as you are within the 6-month retroactive credit window. Just write a covering note asking for credit (and don't forget to enclose a copy of your ticket, and keep a copy of your boarding pass). And even if the boarding pass stub has you BA FF account number, you can explain they rejected the fare, but it is eligible on CX so you're just asking for credit, just as you've just done in your post