A little explanation of cover handling in current Kobo firmware.
- Cover images for kepubs are stored in .kobo/images. They are downloaded from the Kobo server. Deleting them will probably leave you with a default cover for those books.
- Cover images for sideloaded books in the main memory are also stored in .kobo/images. They are generated by the device the first time they are needed. Deleting them will mean they get generated the next time the cover is needed. The cover image is the first page of the book.
- Cover images for sideloaded books in the SD card are not stored. They are generated each time they are needed. And they are the first page of the book.
I haven't seen a problem like what you describe. My first thought for fixing this would be to power off and on. That should clear the memory and cause the images to be regenerated. Another try would be to remove the card and reinsert it. This again should clear the memory as well. It won't remove the details of the books from the devices library, so you won't lose the current reading position.
A more drastic way is to remove the card and insert a blank card. Or at least one without your books on it. This will cause the device to remove all books on the SD card from its database. Then put the original card back in. All the books will be reprocessed and should turn up with correct covers. This will of course lose the reading status for all the books.
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