Clarification of “Clean library…” & help to clean DB

I’ve discovered my database is full of items that have either been moved, renamed or deleted.
I have run the “Clean library” function many times, I’ve also tried an add-on for a deeper clean, without success.

The Wiki says…

http://kodi.wiki/view/Settings/Videos#Library

Quote:Clean library… – Remove items from your library that can’t be found (either renamed, deleted, or on removable storage that is currently unplugged).”

…but it’s leaving behind moved, renamed and deleted files.

So I’ve come to the conclusion that “Clean library” function literally only cleans the library, as in the front-end view, and not the whole database.

Is this correct? If so, without deleting and starting again, is there a way to check every database item for its corresponding file and remove entries when a file is missing?

I run a central mySQL database on Ubuntu, if that helps.

Cheers