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Covers are treated differently for books in main memory to those on the external microSD card. For the ones in main memory Calibre can (if you have the "Upload covers for books" box ticked in the KOBOTOUCH driver) send the covers directly, and they will be saved ready for use when needed. But for books on the external card the covers are always generated from the first page of the book, and they are not saved so have to be generated each time they are needed.
So to get the covers of the books on the SD card to look the same as the ones in main memory you might need to modify the cover in the book itself before you send it to the device. You can do this using the "Polish books" feature in calibre, or the "Modify epub" plugin, or by doing an epub to epub conversion of the book (not recommended as this can mess up other things).
However if you want to keep books on the external card then you will have to make some compromise on the covers, as there are some options that are just not available for those books. For example if the aspect ratio of the original cover is not 3:4 then the cover thumbnails generated from the first page of the book will either be distorted or will have white bars at the sides. But covers for books on the internal memory sent from Calibre can retain their true aspect ratio without any white bars.
If you are using the external micro SD card simply as a way to increase storage capacity, then one option is to replace th internal memory (which is also a micro SD card) with a larger one. That way you can keep all your books in internal storage and not compromise on the covers.
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