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The plugin gets the serial number from the file "version" in the .kobo directory on the device. This also has other information such a the firmware version. The firmware does update this and I'm surprised it hasn't for the cloned device. It might only happen during an sync, or periodically. But, if you delete it, the device should recreate it with the current serial number. Which is what should be displayed in the Device information page of the settings.
The UUID is from the deviceinfo.metadata file. This is created by calibre when the device is first seen. If you copy it to another device, it should be used with no problems. When you add the device in the plugins configuration, it also stores the serial number. If you delete the deviceinfo.metadata file, calibre will create a new one with a different UUID the next time the device is connected. Then, delete the existing devices from the plugins configuration and add them again. That should get the plugin seeing them as separate devices.
The auto-backup should be using the serial number from the version file. It is possible it is using the one from the configuration, but, I don't think so. I'll check when I have a chance.
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