I tried today on the QR website (arriving in DOH on the 18th of November, so just over a week from now). First step is to enter your PNR and last name. I immediately get an error message that my itinerary is not eligible. Although the whole trip was booked on qatarairways.com, the first leg is indeed operated by Sri Lankan, even though it was booked as a QR coded flight. The website error message doesn't specify WHY your itinerary isn't applicable though.

I called RES just to be sure, but the agent didn't seem too familiar with any of this. She said "I dont think the flights matter as long as the layover meets the criteria" or something, which obviously didn't seem right given that the terms do specifically state that both inbound/outbound flights need to be operated by QR. In any event, she didn't have an alternate means of applying for the new VISA so I'm out of luck.

I'm not sure what the difference is, if the whole itinerary is booked via QR and includes a QR-coded flight, they obviously have access to the whole itinerary. But I don't make the rules. oh well.