For anyone else reading this, DO NOT uninstall CS6 until you understand how to keep Encore CS6. There is no Encore in CC.
There is no problem reinstalling it, but you a) must install Premiere CS6 (which installs Encore), then uninstall Premiere CS6, unchecking Encore as part of what is being uninstalled. You can, of course, simply leave CS6 or Premiere CS6 also installed.
I do not have CC, but I believe that, once you are logged into your CC subscription, you can find the installer on line.