Deleting books from CC works for me.
Steps I did:
- Send an ebook to CC from calibre.
- Verify with a file manager that the book is in the Calibre_Companion folder
- Click the book in CC to get to book details
- Delete the book in CC's book details
- Verify with a file manager that the book is no longer in the Calibre_Companion folder
What are you doing that is different from the above? In particular, where are you finding these other copies? Some reader apps, in particular Aldiko, make copies of books. Some others cache parts of the book.