Crazy: I had this issue with vc-state reporting 'edited on a visited file even after all changes made were pushed to the remote Git repository in a commit. Looking for answers in Emacs Stackexchange I find someone having the same issue --in a different context-- but with no replies, the question passed unanswered like six months... until now!. Took me one minute this time (I have been dragging this during two years or so) to find out we had vc-refresh-state which solves my issue and the issue of OP in Emacs Stackexchange.

It was a matter of hooking it with some Magit's hooks and you are ready to go!.