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An e-ink Kindle will find books in subfolders of the Documents folder. When you copy an entire book folder from calibre it will find the MOBI file and just ignore the extraneous cover and metadata files. It is not using that cover JPEG, but instead extracting the cover from your MOBI.
The Kindle app on Fire tablets does not search subfolders so your MOBI must be placed into the main books folder. Again the cover and metadata files from calibre will just be ignored if present.
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