duplicates on hard drive

Hi: Can use help. My hard drive has many, many duplicate directories, and mostly, but not always, duplicate book formats taking up much valuable space. Here is an example: calibre library->author Good up to here. Then, Under the author we have three directories for the same book title (spelled identically) however each directory/book title is followed by a number in parenthesis for example:

book title (1)
book title (4)
book title (8)

I assume this number has reference to adding the book multiple times, however I do use the duplicate plug in then delete dups using delete within Calibre. Looking in each of the three directories, the first only has a file named metadata.opf, the second and third directories have four files: a cover, the same metadata file, and a book file in a epub and mobi format.

The duplicate book title directories are present for the vast majority of author directories with titles duplicated two, sometimes three times.

I do not edit the calibre library directory in explorer, and no longer run Calibre on different machines using the same Calibre library which is on a windows shared drive, just not being used by calibre simultaneously.

When this happened previously, the only solution I could find was closing Calibre, renaming the library directory and using add books to a new calibre library.

As info, I have in configuration the option to check for duplicates.

What could be causing this and is there a better way to fix other than creating the library from scratch? Very much appreciate help!

Regards,

Larry