I have the same issue. I found KLM Business flights from Europe to Africa cheaper on KLM.com(Half the price). So of course I had our work travel agency call Delta to get the KLM flights booked on a 006 ticket.

I was able to book all 3 itineraries on 006 however I am nervous as the flights do not appear on My Trips section of Delta.com

I am going to hit silver based on my Business class flights to Europe on Delta/VA. But my goal is to hit Gold based on my onward KLM business flights to Africa from London and Amsterdam. I am worried the MQDs wont transfer over.

Did you get the full MQDs? According to Delta, KLM partner flights only earn a percentage of MQds but its unclear if this is also for 006 tickets booked through Delta. And why does Delta.com not show all Skyteam flights? KLM and AF both have the ability to show Delta flights. Seems like their systems are more sophisticated.

Here is a rundown of my itinerary.

JFK - LHR Business Z Class on Delta
LCY - AMS Business J Class on KLM(Operated by Cityjet which may not get credit??)
AMS - EBB Business Class J on KLM
EBB - DXB Emirates
DXB - AMS Business Class J on KLM
AMS - LHR Business CLass J on KLM
LHR - JFK Business Class Z on VS* Codeshare

Im going to need the full MQDs to reach Gold(Just shy of SIlver now). Im not worried about MQMS.