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The message is letting you know that the "dirty bit" is set on the drive. I used to get this a great deal on my Kobo's regardless of how careful I was in removing them from my PC. (The safe remove external drive stuff).
I normally would allow Windows to do its scan / repair of the drive.
However a few Kobo releases ago some of the Linux components of the firmware were updated and since then I've had no reocurrences of the issue.
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