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I had a similar issue. I deleted the all of the books off my Kindle to reload them in bulk from Calibre after cleaning up the metadata. After doing this, I noticed that the available memory was not what it should be considering there was nothing on the reader. Restarting the Kindle didn't affect it. After a support call to Amazon, I was advised to "Reset to Factory Defaults". (From the Home page, Menu, Settings, Menu, Reset.) Since I had nothing on the reader, I wasn't going to lose anything anyway, so I tried that. It did the trick - I had all of the memory back. It appears that the Kindle doesn't really delete things when you delete them, even if you don't have any access to them!
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