Had this same issue when flying to Hawaii 2 years ago. The flight I booked from MSP-LAX-HNL had the same flight number, so I was not upgrade eligible. When I went to select seats, only one flight appeared - MSP-HNL - even though the flight stopped at LAX.

The Diamond agents were unable to do anything. As a result, I e-mailed Delta corporate. They called me back a few days later and rebooked the flight point to point, which fixed this issue. They also told me in the future not to book flights that continue on with the same flight number.

I then was able to secure the upgrade on the MSP-LAX and LAX-HNL flights. I'd call the Diamond line and see if they can separate out the flights and rebook them point to point. However, I'm not sure if you'll have much luck.

Good luck getting this figured out.