Unrelated. The apnx files handle the page numbers, not the covers/thumbnails.
For 'fresh' sends of new books through calibre, there are no issues anymore. If you're updating a broken book, you may indeed annoy the Kindle catalog (which in turn can cause the broken thumbnails issue) by doing it without deleting the book from the device UI first, so that's my usual answer.
(If you have a lot of books to update, you can do it in two passes: plug, mass delete, unplug, plug again after the UI fully refreshes, send updated copies through calibre).
Last edited by NiLuJe; 09-15-2013 at 02:43 PM.
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