I have exactly the same problem with my Paperwhate, thought it might be better to post here than to open a new topic.
So suddenly my Kindle started showing that there are 0 files on the device. However, when I connect it to PC all the files are there and I am able to open them in calibre (so they are not corrupted). I am also able to transfer new files to kindle without any problem, but when I manually delete and send (via calibre) books that I have already had on my device, they still do not show up. I guess indexing is also a problem here.
Is there any way to restore my previous library without losing highliths and metadata? Is it ok if I just try to manually backup all the files that are on kindle, reset it, and put them back again?
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