I'm having the same problem with a TACA flight. At online checkin I entered my A3 number and it was stated on the boarding pass as well as the silver status. Miles were credited to my Lifemiles account though. Any chance to get the miles transfered to A3?

Now i'm having an AVIANCA flight in 2 weeks on a different ticket. While booking this ticket I didn't enter any FFP numbers, but I already did checkins on previous flights on the same ticket with my A3 number for EZE-MDE on AVIANCA but also with my lifemiles number for the flights MDE-LIM on Aerogal because that flight wouldn't earn me any A3 miles. Now i checked on checkmytrip to see that both FFP numbers are stored.
What is the best way to make sure that the next flight will be credited to A3? Don't do online checkin and tell the CI agent to delete the lifemiles number?