I was cleaning my drive and removed many file duplicates. I removed many photo masters (originals) from OS X Photos app library, but when I open Photos app I saw that all photos are still in my library. Is there any way to delete photos without masters from my library?
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.