For me, the greatest problem is the highlights. The footnotes thing, once you go to kepubs, only has the refresh bug that - annoying as it may be - at least has a workaround.
As for the notes/highlights, when they stop working... They just stop working. Since the books I've been reading really require me to take notes (and follow footnotes), it has been a fairly bumpy first kobo experience.
On the other hand, my gf mostly reads novels, so she's over the moon with her Glo HD. So I'd say most people don't experience my level of frustration...
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