@maliciousloki: There's a FAQ entry for this, but, basically, there's far less tedious workaround:
Enable the 'Enable sharing of book content...' in mobi/azw8 output settings.
With that setting, Calibre won't set EXTH 113, which in turns makes the Kindle generate the thumbnail itself.
Granted, on the PaperWhite, that might also mean ending up with the file flagged as PDOC.
Note that Calibre also sideload a thumbnail itself, which might not be properly sized/formated for the PaperWhite, which is why with a book with EXTH 113 set to something other than an Amazon ASIN (like the UUID Calibre uses and rely on) you get a broken thumbnail, while this workaround is perfectly effective on the Touch.
Now, a couple of things to understand about what you did: you effectively prevent Calibre from identifying the book on your device via its UUID (it's, among other things, used to match a book on device with a book in your library). Calibre will fall back to other metadata to do this match, sure, but it might be less accurate, less efficient, and probably will break if you use a metadata plugboard.
(And, FWIW, the only thing needed to achieve what you wanted are: set exth113 to the real Amazon ASIN. Delete the thumbnail and rely on your Kindle wireless connection to pick it up (if the ASIN matches) or upload it yourself.)
As I've said in other threads like this, I will look into updating the 'let's sideload the thumbnail ourselves' workaround for it to work properly on the PaperWhite, if possible, as soon as I get mine.
But basically, right now, you've got two 'easy' choices:
* Check 'Enable sharing of book content...' in mobi/azw3 output setting. You get a working cover, but a pdoc tag, and no syncing.
* Send your book to your Kindle email address. You get a working cover, (a pdoc tag?), working sync, it clutters your Cloud drive (that might be a plus for some ^^), but you can't send AZW3 files.
Last edited by NiLuJe; 10-07-2012 at 08:23 PM.