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Hmm, I'm thinking -- is Calibre still recognizing your Kobo as the same device? After my Aura HD reset itself, I had to re-add the device in a few config dialogs or some of the plugins failed to detect it - Kobo Utilities and Reading List specifically.
I don't know that the KoboTouch/KTE driver has device-specific settings though, which is where this falls apart.
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