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The database is checked using the Check device database when a Kobo Touch ereader is connected.
To store and restore the reading position information, you will need to configure KoboUtilties. See the attached image for the configuration I use. Once that information has been stored by connecting your Kobo ereader, it can be restored after a reset by using the Restore option in the Store or Restore Bookmarks See attached image.
And yes, I would recommend manually updating your Kobo. Please note that firmware update can no longer be done through calibre since Kobo has made changes in their web setup.
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