I had a problem recently with my Glo where each time I connected to the PC, Windows would tell me the filesystem was dirty. The solution was to do a factory reset. This formatted everything and once it finished updating to 3.0.0, it was OK.
Do you have another computer you can test with? If so, see what it says. It shouldn't be any different, but, it could be a sign of a problem with the PC rather than the device.
If it happens on another computer, I think I would let Windows do what it wants. It should only be able to access the user portions of the drive. Reformatting will wipe the books and the database. When you disconnect, it will take you through the setup again. Hopefully, everything will be OK after that.
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