Are you using Kindle for PC as a reader or just for the purpose of getting the books into Calibre? I'm using it just to get books into Calibre, so I just empty the KPC folder and download the book I want. That way, there's no question that you have the right one for the import. If you do use it as a reader, but you want to import one book, move everything to a temp folder and download the one you want, import it, then move everything back. If you want to import everything, then it doesn't matter. Just select all of them.
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