After having been through that particular bug with my Kobo Glo readers on an AMD 64-bit Windows 7 machine, I think the warning should remain. I can definitely say it was not a Calibre issue, but a Kobo issue, since Windows Explorer also wouldn't work. My fix was downgrading to a much older firmware on the reader and staying with it for over a year.
The warning is valid since it seems to affect people and readers randomly. Just because it hasn't affected you doesn't mean there isn't a problem.
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