I've never known it to be possible to remove/replace the Frequent Flyer number in the manage my booking section of either the KLM or Air France websites.

I've just looked at my upcoming reservation on the KLM website, and it has my Flying Blue number but there is no way to remove it/change it. On the Air France website, for the same booking, it says "Frequent flyer card : Not specified " and there is no way to add one!

Anyways, it's possible to get your status corrected on the boarding pass when you arrive at the airport - if you're checking in luggage, then you'll be speaking to an agent anyway and can get them to do it. If you're worried about potentially missing out on an upgrade - I think you can dream on!