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In it's internal file store Calibre always stores a cover.jog. This is in addition to whatever is sorted inside any particular eBook file. This is done as many ebook formats do not support string the cover image, and calibre stores all formats for a given book in the same folder. The cover.jpg file is the one used in the calibre GUI. It need not be the same as the cover image stored inside any particular eBook file.
You cannot change this behaviour. However since you are not meant to be accessing the internals of the calibre library directly this should not concern you.
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