Hello tas,
I haven't gotten to play with the newer model (Glowlight Plus) yet. But moving the books around may well confuse the issue. On my older NOOKs I think the cover thumbnail is created when the book is first added. If you can find the .docThumbs folder, delete any thumbnails from the affected books, then delete the epub files for the books involved. Power the reader off and back on, then add the books back to the folder you want them to be in.
Those thumbnail images in the .docThumbs folder must be linked (somehow) to the epub. When you moved the epub it might have broken that link, that is, the reader is looking for a thumbnail with a different name, but it was never created because they only get made when the book is initially added to the device. This is all guesswork on my part, of course.
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