I have a question for the experts regarding KLM codeshares on DL tickets. Thanks in advance.

Background: I am flying with a family member from the US to CPH in two months on separate PNRs. On the return, a major schedule change rolled out this weekend to the final domestic leg from DTW forced us to have the routing changed to CPH-AMS on KL, AMS-ATL on DL, then one more DL flight home. Because there were two separate PNRs, the agent had to work on them one at a time. For some reason, on the KLM flight, the agent booked me on the codeshare flight (DL 9xxx) in Y class and put the family member on the actual KLM flight (KL xxxx) in M class. The original tickets were booked in U on DL. The tickets got reissued about 36 hours later and still reflect Y on DL for me and M on KL for the family member for that segment (DL U the rest of the way)

Question: Could there be any issues in starting the return with one person on the DL flight number and the other on KL? I'm thinking check-in, seat assignments, checked luggage?

It appears that M fares on KL earn full mileage and 150% MQM (same as DL Y), so there shouldn't be an issue with miles. In fact, we might get a few bonus MQMs over the original U fare.