I've had this happen to me when I got rebooked due to a delay. If I recall correctly, I submitted this form:
https://www.delta.com/contactus/page...=mileagerefund
and explained that I did not receive credit because I was rebooked due to a delay. It took a week or two, but I did get the credit. I was on DL metal, so it may have been easier for them to research versus your experience.
This was exactly the issue! Thanks so much. It was confusing because on the website, it stilled posted the MQM and MQD for the leg where I got rebooked. When I looked into the receipt, I noticed it said PRNT instead of FLWN like the other legs. Called Delta to explain this and they were able to process it. Finally hit PM now!