I had this happen recently also. Had my AS FFN on the boarding pass and it was still credited to BA on the outbound. I made it clear to the check-in agent at my outbound airport and at customer service in the First lounge to make sure my AS FFN was on there and both had said it was on there. Few days later, my return also credited to BA. I called BA to have them uncredit both the outbound and return, which they did. Yes, contacting the executive club by phone is the best way to do it.

I usually don't make changes to the FFN but due to the recent changes by BA on the qualification period. I shifted them to AS.