That is to do with how the Kobo devices handle books. When a book is first put onto the device, it gets processed. The device extracts metadata from the book and puts it into an internal database. This database is read when you are using the device. The library list with the details come from this. If you replace the book later, the device doesn't reprocess it, so the metadata isn't updated.
The cover images are generated when the device needs them. They are the first page of the book. Once the cover has been generated, it is stored for later use. This means if you replace the book with a new version that has a different cover as the first page, the cover the device shows will not change. You can get around this by selecting the "Upload cover" option in the driver configuration. With this selected, the driver replaces any existing cover on the device with the one from the calibre metadata. There is also an "Always upload cover" option that gets the driver to upload the cover even if it doesn't already exist on the device.