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For the series information to appear, you'll need to connect your Kobo to calibre for the second time after transferring the books, ejecting and disconnecting. And don't use Collections/Shelves for series, that information is outdated. Calibre will set the series based on the series column.
Do you have
1) metadata management set to Automatic in Preferences -> Sending books to devices?
2) the following fields checked in the Kobo driver settings: Update metadata on the device and Set series information?
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