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SmartEject's settings can be found by opening Calibre's Preferences -> Plugins, then search for SmartEject.
I don't know of any reason why either SmartEject would treat a device differently after an update, unless you changed it's search settings to be specific to the device some how.
Is that Kobo version extremely new? I know that Calibre has more code and plugins specifically for Kobo than most other readers.
For Reading List plugin, it might help to instruct RL to recognize the device. While it's plugged in, go into RL's customize/config go to the Devices tab and click "Add connected device".
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