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Yes, Calibre updates metadata for the books on the device, but only if it's aware that the book is already on the device - otherwise it creates a new entry. If you had your books on your Kobo, but they were not matched to the ones in the library, Calibre had no way of knowing that they were the same books.
There are several solutions.
- delete the books from your Kobo before sending the updated copies, or
- when you connect your Kobo to Calibre, you should see green checkmarks for the books on the device (in library view). If there is no green checkmark, then either the book is not on the device or Calibre doesn't know it is, in which case you need to use Match book to library to let it know.
Also, you might want to check "Don't treat replacements as new books" in the Kobo driver settings.
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