I suffered a severe shoulder injury (multiple fractures) in 1995. Opted out of shoulder replacement. About 60 days post-injury, we flew LAX/PPT on AF. I asked the FA for a bag of ice and extra pillows on which to rest my "bad arm." The FA was very accommodating. The extra pillows made a big difference, in that I was able to keep the arm somewhat elevated. Of course, now that so many airlines no longer offer pillows, I suggest bringing your own to put on the arm rest.
Good luck