This happened to me quite often and what I discovered is that I was not going through the correct process to safely remove the device. I had the computer scan and fix the drive (Kindle) and now when I am ready to disconnect my Kindle, I click on a small icon and the computer asks "Do I want to remove the device" to which I click YES. Then I get the message I can safely remove the device. Since doing this, I no longer see that scan and fix message. I could be wrong but I think just unplugging the device without safely removing it, could be the problem. Just my two cents.
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