This year I had similar issue. I had W fare ticket with TATL flights operated by AF. I wanted to use my SWUs but declined by DL.

After some changes in flight schedules I made several tries to change my ticket to DL operated flights (class of TATL changes from W to Y since W is not available on DL flight) and apply my SWUs... Took while to find the right customer representative. There were some problems with tickets then, but local DL representatives helped me to ticket it. It was paper ticket, but happy to had it. Was little nervous until departure but no problems then.