Just went through this debacle with Delta. Short story is, if its marketed by Delta with a DL flight number, all paid upgrades should get a MQM bonus based on class flow, not paid. However, MQDs are only provided for upgrades if purchased through a Delta channel (Delta.com, Delta App, etc).
I flew from BCN to SEA, with a connecting flight in CDG. My flight was both ticketed (006) and marketed by Delta (DL), but I used the Air France website to check-in and purchase a business class upgrade from CDG to SEA, putting me in a J class. Per Delta's guidelines for Delta marketed flights:
Purchased upgrades are eligible for bonus MQMs based on the class of service flown. After the Skymiles credits were processed, they only issued me a 100% MQM accrual, based on my paid class (Q), which was not correct per their program guidelines.
I called and talked to a Skymiles rep, who confirmed that it showed my class flown was J and issued me the 200% MQM accrual as it should have been. However, I did have to send in my Air France purchase confirmation to show that I actually paid for the upgrade vs getting a complimentary upgrade. I was only 4,000 MQMs away from qualifying for diamond, so I might have pushed a bit more than usual to make this happen.
