I can see why theducks posted that link, but from your posts, I don't know what you are doing and what is happening.
As the theducks said, you will have directories called "unknown" if the books in the library do not have an author or title. To fix this, you need to fix the author and titles in calibre. calibre will then rename the directories and files as appropriate. If after doing this, the "unknown" files and directories still exist, then there is a problem.
If you directly edit the directory and file names, then you will break things.
So, what are you actually doing when these extra files appear? Or don't disappear.