Had this problem out of Amsterdam a few years back... Whether by error or laziness, the KLM Check-in agent while tagging my bags wanted to charge me for my second bag. After pointing out my PM status, she made some changes and finally checked my bags in only to find out later that she had substituted my Skymiles number on the flight to my Flying Blue Account number.

Long story short, Contact Air France Flying Blue, advise that you want the miles from this flight transferred to your Skymiles account and cancel your account with Air France. You will have to contact them again and provide proof in the form of an email confirmation of the cancellation of your Flying Blue Account and then formally request the flight segment mileage/credits to be deposited in your skymiles account. Stress that the names on the other Flying Blue Accounts will not match the names of the persons that actually flew the flights. Make PDF's of the emails and submit unless you want to chance faxing in the necessary correspondence. Short of following the steps they request, there is no other way of getting credit for those flights affected. Believe me I tried...The steps are required I was advised so that people do not double dip on the mileage/credits. Doesn't make sense if it was their error, but like most things, "Give unto Caesar what belongs to Caesar"...Hope this helps..