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You will need to first connect and send to device after which the book will be imported. After tha, you will reconnect, hopefully with metadata management set to auto (Preferneces => Send to Device => Metadata management => Automatic management. You need to have the book imported to the Kobo device's database before calibre can update the metadata such as page counts, series/index, etc. I'm assuming that you have the KoboTouch driver configured to send the series information on tab 3 of the driver configuration dialog.
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