We ran into similar issues internally and so we changed how the bindings mechanism works for 4.16. You might want to try and upgrade to that when it comes out (soon).
Basically, what you’ll want to do once you upgrade to 4.16 is to run this menu item once on each level sequence, “Rebind Possessable References”. That should upgrade the bindings mechanism to the new one and should be much more stable. In 4.16 any new bindings that you create will be with the new mechanism.
