Joints do have a nasty tendency to wear away with time, unfortunately. I think all the advice above is sage and will help a lot. You need to not only prevent pain/discomfort in the here and now but also prevent any damage getting any worse in the future.

You thought about doing a set of standard warm up/cool down and strech exercises before, during and after any bondage session? This may minimise discomfort. Also, look into massage techniques to help with those trouble areas. There may be something your Dom can do to you before or after a session to ease the pain of those joints.