Flying Blue's T&Cs specifically state that you can only utilise one frequent flyer programme per booking.

Do you really need to have both a Flying Blue account and a Skymiles account? If you do, I would advise you to separate them more fully/completely; remove the FB number from the "other loyalty programmes" field, and consider them as two completely unrelated entities. It doesn't work quite as smoothly and seamlessly as you seemed to think in your OP; it therefore requires you to think a little harder and adapt your booking behaviour to reflect the reality of how running two programmes actually operates in real life.

You can book flights (on either Delta, on AF/KL, or on any combination of all the above) *without* being logged in to your account. This means that no FFP number will be associated with the booking. You can always add an FFP number to the booking later, but once an FFP number is associated with a booking, it is extremely and annoyingly hard to get it changed in a way that actually works in the way you intend. Simply asking the check-in agent to change the number, and seeing the "correct" number/status on your boarding pass, is unfortunately not a good enough guarantee that the miles will not end up going to the "wrong" account anyway. If you intend for your own reasons to maintain both a Delta Skymiles and a Flying Blue account, it may behoove you to make all flight bookings "blind" (or, at least for the bookings for which you anticipate that you may wish to change the FFP later on) and only later (perhaps as late as check-in, or even after having flown) deciding which FFP number to use.

We have frequent reports over on the Flying Blue forums of people who, like you, have both a Skymiles and a Flying Blue number, and when they fly with AF and/or KL, the miles end up in the "wrong" account. I suspect that people that use an AF or KL app to manage reservations that include, or are solely, on those airlines, at some stage ended up signing up for a Flying Blue account, rather than just making a profile to use the app. The Flying Blue number is incredibly "sticky" and in cases where a booking gets associated with both a Delta Skymiles and a Flying Blue number - even unwittingly, i.e. by using an AF or KL app to check in or assign a seat, when that AF or KL app knows you have an FB number and it logs in you as an FB member - the miles will frequently end up in Flying Blue rather than in Skymiles, where the complainant expected them to end up. This is even more critical now as FB recently changed its T&Cs so that flights/sectors that post to Flying Blue can not be removed for the purposes of recrediting them to a different FFP - even if the sector in question didn't earn any miles in Flying Blue.

So you will just have to resign yourself to the fact that you cannot use the status perks of a Flying Blue account on a Delta flight if you actually want the miles for that flight to post to your Delta Skymiles account.

Again, I would advise you to reconsider having both programmes, but if it makes sense for you, just get used to the reality that you can't mix/match/merge the two and need to operate them separately.

https://www.flyingblue.com/kamino/policies/us/en