The only time I ever lost root on a phone was when I installed Airwatch for corporate email and apps and stuff. I didn't -know- I was losing root or I never would have done it. Strangely everything that was previously granted SU access worked, but any new requests were not processed.
Have you installed any apps or changed anything else in your system? What method did you use to root?
Is SuperSU just being removed, or it stops working? Sounds strange for sure.