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A number of months ago I was browsing through the files on my Paperwhite and discovered a bunch of garbage files in some of the hidden folders and under /system. I recovered about 300MB after (carefully) deleting them (they had suspiciously old dates and filenames that referred to items that were no longer on the Kindle). Unfortunately I don't remember the details. They were probably left around after abnormal restarts (of which I had a few in the first months I had the PW), or possibly bugs that caused them to remain around when they should have been deleted.
I've never used calibre with my Paperwhite, and only rarely transfer files over the cable, so whatever the problem was it was, it was Amazon's doing.
But you might look through and check. Make sure you set Explorer/Finder to view hidden folders/files.
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