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I download all books to my Kindle Touch, back them up (including the Real Page Numbers and Public Highlights and stuff) then import into calibre. I manually add the original filename to a custom column in calibre, then use that as the save template for the Kindle driver.
Then I edit metadata 'til I like it, and send the book from calibre to my Kindle. The previous steps allow the book to overwrite the old copy, rather than adding a new copy which doesn't match the sidecar files.
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