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Did you double check the configuration settings for the Kobo Touch driver in calibre?
You can access them a couple of ways; Preferences | Plugins; select Kobo Touch under Device Interface and customize driver, or with the device connected, the Configure this device option on the drop down besides the Device button.
In either case, if you want to use collections on the device ensure the calibre column names are specified. If you want to read in kepub format select the option Use Kobo viewer for EPUB books (all on the Collections, covers and upload tab). To support series you need to select the series options on the Metadata, on device and advanced tab.
Additionally ensure that in calibre Preferences| Import/Export | Sending books to device that the option Metadata Management is set to Automatic management.
Also remember that some data (for instance series) is only synced AFTER the Kobo has successfully imported the book; i.e. after sending a book to the Kobo, disconnect the Kobo and let it import the book and then reconnect the Kobo and eject a second time.
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