(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!