Hi guys
I have this problem (i noticed that today but i thinks this problem has arrived when i update OS to Sierra).
I have installed xcode with ElCaptain and i don't have any problem when i opened the Apple Store for update it.
But today when i open the store xcode is like never installed but is really installed in my mac!
If i click the button for install OS install another xcode!
I do not want to reinstall it if not necessary
in link an image: