I am currently dealing with the same thing. I had LAX-AMS-BKK-AMS-LAX all credited to Flying Blue instead of skymiles. I am not going to let this go, because I did absolutely everything right.

When booking, I made sure only skymiles info was in. When checking in online, I made sure I was not logged into flying blue. When I checked my bags in at each airport I made sure no flying blue info was entered in system, and confirmed that symiles info was on each boarding pass. I am extremely aggravated as I may miss out on Diamond status because of this.

I can say with certainty that you will get nowhere by calling/messaging/emailing Flying Blue. I am currently reaching out to several Delta and KLM contacts with copies of my boarding passes all showing the skymiles info. I'll let you know who ends up resolving this. What a drag.