1) Reboot your Kindle (Menu => Settings => Menu => Restart)
2) Plug the Kindle into your computer. Check the documents folder -- are the ebook files you added still there?
...
Note that calibre does not interfere with the Kindle database (which is kept on a hidden partition). It only copies over ebook files, which at worst will mess up one book.

Also, LibrarianSync is pretty well-tested, so I doubt it was a problem with LibrarianSync either.