How to remove photos without masters from library in OS X Photos app?
Photos should detect when changes have been made to the library and prepare it for you. See Photos has attempted to repair the library.

You can force Photos to repair the library if it doesn't do it automatically:


  You can force Photos to try to repair the library by holding option and command (⌥⌘) whilst launching Photos. Photos.app will try to repair the library and it may ask you for administrator privileges.