After more than a year, this issue still hasn't been fixed.

The condition to trigger this issue is relatively rare, but it's certainly making SEs life (or anyone who has PRs to burn) harder.

If you have a partially flown PNR, and the change you are trying to make involves a stop-over fare (the one with 5000 pts surcharge to allow you make a stop of up to 45 days along the routing), then the auto-pricing system would calculate ADCOL based on the price without priority rewards. The worse part is that auto-pricing system would indicate PR has already been factored into the calculation, so even if you escalate to a supervisor, they may just tell you to "go pound sand". The prompt to potentially make a supervisor aware of the issue is to kindly ask "could you price this manually to see how much it would cost without a PR", and if you are lucky to get a competent supervisor, they will notice the issue and manually half the price from the manual-pricing.

Context: I booked AAA-BBB-CCC, CCC-BBB-AAA RT trip, flown AAA-BBB-CCC, then tried to do a stop at BBB by moving BBB-AAA to a few days later. I first removed BBB-AAA and it was fine, got no difference in points and got a few dollars back in tax (CCC-BBB and CCC-BBB-AAA are in the same distance band). Then when I tried to add BBB-AAA back, if it's within 24 hours of CCC-BBB (no stopover), then auto-pricing works fine. However, when trying to add BBB-AAA more than 24 hours after CCC-BBB, the auto-pricing system starts to quoting price based on non-PR rate.

I asked the supervisor to file an IT ticket for this but not sure if it will ever get fixed. If someone here has better contact inside AP, I'd happy to provide a PNR as a reference to look at.