[itimpi]

If you delete books via Windows Explorer rather than via Calibre it could explain your symptoms. Calibre will be looking in the metadata.db file to see if it has specific formats - not directly at the hard disk itself.

You could use a tool like "Remove Empty Directories" (a useful piece of freeware) to scan for folders that are empty (except perhaps for the cover.jpg file). Just use the scan option and not do the actual directory remove unless you really want to.