I have a booking with legs on SK and AC and have used the feature in the SK app to set a different FF number on each segment. I see in the cowtool that both FF numbers are associated with the booking but I'm wondering if you can see how they have setup the SSR. Ideally I'd like AC for FQTS and SK for FQTV on the two SK legs, but I'd settle for FQTV to be properly set to the operating carrier for each leg.
I've had issues with Concur setting 2 FF numbers before, with the segments being credited to the wrong airlines so I'm hoping that the SK app does a better job of it.