And you don't have to jailbreak your Kindle to remove the "sidecar" folders. In my experience, these are deleted by Calibre when I use Calibre to delete the book from my Kindle. Not sure why Mendesitba's experience is different than mine. Maybe it's because I use Calibre to add all books and delete all books from my Kindle.
If you do have extraneous "sidecar" folders remaining no your Kindle, you should be able to access these through Windows explorer (or Mac or Linux equivalent) and delete them from there.
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