Sounds somewhat similar to an experience I had a few months ago. Not sure whether you recall the post, but after getting a similar runaround, when I went back to WS and insisted that everything was 100% correct on the OAL end (AF in that case), and that they were 100% certain the issue was at WS, someone at the WS support desk "manually" fixed the PNR to match AF. Although that first WS being missing is different from what I went through, so I'd be a bit more concerned.

Given that the issue has always been on the WS end in my experience, I'm inclined to look in their direction again. But to be clear, the Amadeus PNR doesn't have any of these unconfirmed (UN status) segments still on it? If you can check (I'm not sure whether TripCase would be able to see these), or have a QF agent check (they would definitely be able to see), that everything is clean on their end, I'd probably call WS again and insist that they fix it.