In calibre, with the device connected, go to device list. Find the book that doesn't match the library and right click on it. One of the options is something like "Match to book in library". Select that and a search dialog comes up. Find the book, select it and press OK. After you do them all, right-click on the device button and choose the option to save these changes. Sorry, I can't check what it actually says at the moment.
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