Two points:

1) because these bookings now apparently know of both your Skymiles number and your Flying Blue number, the miles could end up in either account, i.e. there is a good chance that the miles will end up in the wrong account. In future, refrain from "polluting" the booking with anything other than the account you want the miles to end up in. If you want Delta flights to post to Flying Blue, do not book the flights while logged in to your Delta account, and do not view, manage, or in any way interact with these bookings while logged in to your Delta account.
You may, for example, decide to book the Delta flights from a third party, and refrain entirely from viewing/managing/looking at these bookings via the Delta website.
This includes checking in; make sure you are not logged in to your Delta account if you check in online for these flights. Do not use the Delta App to check in for these flights and do not use the Delta App to show the boarding passes for these flights.

2) Any Delta domestic flight - even a transcontinental - will earn only 2 XP (or 6XP if booked in Delta's equivalent of Business Class).