The important part of Find Duplicates>Binary Compare is to set the appropriate Result Options for how you want any duplicates to be handled. Really this comes down to two means of cleaning with Binary Compare:
- Automatic Cleaning: You trust the plugin and just want it to delete any duplicates. Check Automatically Remove.
- Manual Cleaning: You don't fully trust an automated system and want to manually pick and choose what is deleted. Check the options Show All Groups At Once and Sort Groups By Number of Duplicates, at least.
For manual cleaning (sorry, I'm paranoid and would rather choose for myself which items to delete), your book list is set to a Virtual Library (duplicates only) with a set of duplicate books highlighted. A dialog pops up telling you the total number of duplicate file
sets that have been found. (It's not a total count of all the duplicate books. You could have three sets which involves 52 books because you entered the same file repeatedly under different info.)
You will notice that their are two or more books highlighted: the book you chose and any duplicate books. You can take a look at the individual Edit Metadata, Book Details or Book Pane for each book to determine which book(s) to keep or delete.
To delete a specific book, highlight it in the book list. Then use the normal Delete menu bar option to have calibre permanently destroy the info in the database (ie, the metadata), while sending the ebook files to the recycle bin.
Note: Be very careful to compare metadata. You might have the same ebook file, but different metadata for each ebook entry. They might have different information (maybe one has an ISBN and another does not). Or maybe you've got two different publishers and published dates. Or the comments are different. So look at everything and make sure that what you're deleting is the one you really, really meant to destroy. Also be careful for things like the book variations: the normal edition or the 20th Anniversary edition, normal or illustrated, 1st or 2nd edition, etc.