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The first connection adds the book to the Forma. When you eject, the Format adds the new books to the database. The second connect lets Calibre (with Kobo Utilities plugin) see the books and add the metadata to the database for the newly added books. You do not have to add any more books for the second connection to get the metadata added as long as are set to Automatic management.
You also need to have Metadata management set to Automatic. That is found in Preferences > Import/export > Sending books to devices.
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