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Originally Posted by DNSB
As near as I can tell, my Kobo does not display the covers from an ebook in the internal storage any differently from a cover from an ebook in the external storage.
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The difference is only if you are using Calibre to send the covers seperately from the book, which can only be done for the books in internal storage. The covers sent by Calibre don't have to be generated from the first page of the book, so they can have any aspect ratio without being stretched or filled out with whitespace. The Calibre-sent covers can have the same look as for kepubs downloaded from Kobo, something that can't be achieved for covers generated from the first page of the book.
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This can result in letterboxing (horizontal) or pillarboxing (vertical) bars if the orginal image is not in a 4x3 format but I'm willing to live with them rather than a distorted apect ratio which bothers me even more.
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Sending the covers seperately using Calibre avoids both the letterboxing and the distortion.
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I still suspect that removing the books from the internal storage before copying them to the external storage was not done properly which can lead to all kinds of nasties with database corruption. Been there and done that, got the factory resets to show for it.
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You might be right, it depends what the OP means by "messed up" I guess. I always use the delete function on the device to delete books myself.