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I can't find any setting on my Paperwhite that can identify what I copied from Calibre vs what was downloaded from Amazon.
The only options in the filters for "type" are: books, samples, documents, newstand, audible, comics and collections.
Books which I purchased from Amazon but copied to the device from Calibre show up under the "books" type - as do the books which were sync'd directly from Amazon to my device.
I looked up the date when I purchased the Paperwhite. So far, of all the books I've checked, books purchased before the Paperwhite (which would have been copied to the device from Calibre) are gone.
All of the books I've purchased after getting the Paperwhite (which would have been downloaded directly from Amazon) are still there.
So it looks to me like all books that I purchased and copied to the device via Calibre were deleted.
Of course, since I purchased them, I can re-download them from Amazon or re-copy them from Calibre but I think Amazon removed them because I can't come up with any other theory for why 1300 books disappeared from my device.
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