Sorry, at this stage I've more questions than answers:
- Did the Kobo have any hacks or tweaks installed, or was it standard factory firmware?
- Did you double check (in the Finder, or with whatever Windows calls it - Explorer?) that the Kobo was fully ejected from your system before unplugging?
- Can you post a photo of the screen?
If a full charge and pinhole reset haven't worked, the next step is a factory reset.
I confess that I avoid Kobo Desktop like the plague since it became unnecessary, so I've no personal experience to share with recent updates done that way. I always use over-the-air updates now.
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