mmm with my Kindle books, I download them to my PC and import them into Calibre. I've not had any problems with book organization and then uploading/sideloading them to my Paperwhite or my tablet (Lenovo).
EDIT: after re-reading your post, I'm thinking you want to maintain the folder structure you created in Calibre. I don't think that's possible, at least I was never able to figure that out.
Last edited by GlenBarrington; 03-10-2018 at 03:41 PM.
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