This is explained in more detail in other threads but basically here's a workaround fix. In Calibre before you add it to your NC but after you have the cover in Calibre as you want it, convert the epub book to mobi, delete the epub, convert the mobi to epub, & use Calibre add the new epub to your NC. This has been the most successful workaround.
Other things that sometimes works are 1) convert epub to epub, or 2) reboot your NC ( it's been said that with this #2 method the covers will sometimes disappear again.) I use the main method above & it has always worked for me.
Note, books on your SD card will not show up on the NC's shelves in any case, either with or without covers. They will show up under "My Files".
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