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What format are the books in that you are using in Calibre?
There a two different syncs it will do when you plug in, one for the desktop and one for your Kobo. After it has stopped saying that it's syncing try pushing the sync button in the top right corner of the screen (Desktop app, I think that's how you are syncing right?) and then wait until that's done before ejecting and unplugging.
Hope that helps.
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