(I haven’t had personal experience with this, but have read that the Flying Blue number overriding your DL number can cause problems for crediting miles later, and it’s good practice to keep a paper copy of your boarding passes in case you need to contact them about miles credit after the flight. I believe you want your SkyMiles number on the boarding pass, and if your flying blue number shows up you might need someone at the airport to switch it for you ).
For the future, I believe the general advice is to never log in to a Flying Blue account while doing anything with a ticket if you want your SkyMiles number attached to it!
Thanks for the advice, if I do this again it makes sense to not log in. I was thinking it would make sense to have your AF profile (ex. passport #, etc.) saved to make it easier.
I couldn't get through via the phone late tonight but I'll try again in the morning. Also good to know that there's a chance to add it at the airport.
In the end it wouldn't be the end of the world to miss miles, but this shouldn't have been so hard. Thanks again to everyone for the help