If you haven't already done so, try installing the
calibre Kobo Utilities plugin. When the device is connected it has an option 'Upload covers for Selected Books'.
To the best of my knowledge, when you send new books using the normal calibre send-to-device option the cover thumbnail automatically gets sent if you've ticked the appropriate option in the Kobo device driver config. The factory reset probably deleted all those. Given time the Kobo can re-extract the thumbnails from some formats (e.g. epub) but maybe not all formats. The Kobo Utilities plugin just makes it quick & easy to resend the thumbnails. If I've got any details wrong I'm sure someone will correct me.