To counter this, I flew ATL-SEA on DL and SEA-ATL on AS every week for a few months in 2015 (the DL flight times for the latter were not sufficient for my client's needs). For the AS flight, I often got upgraded to FC, which rebooked my flight as a U fare, which is ineligible for mileage accrual per DL. However, my flights were booked in eligible coach fares (T, Q, etc.), and mileage accrual is supposed to be on class booked, rather than class flown.

I asked @DeltaAssist and I called the PM line, offered to show both my receipt and my BP, and both said "Based on your fare class on your BP, you are ineligible for SM accrual on this ticket." For some reason, though, filling out the Request Mileage for Past Trips on the Comment/Complaint form and only attaching my flight receipt (not my BP) would get the miles posted in ~24h, no questions asked. (I always offered to send them the Passbook version of my BP, if needed, but they never requested to see it.) YMMV, but this worked for 10+ trips in a row.