Calibre does write to the disk when syncing. After reading the database on the device, it updates a couple of files in the root directory of the device. And it might update the database on the device. Whether it does depends on some settings. If you send a book to the device, it writes a copy of the book to the device and again, might update the database.
All this should leave the device driver clean if you eject it properly. You need to make sure all calibre jobs have finished and then eject using either calibre or the safely remove device in Windows. It is working with no issues for me in Windows 7, but I haven't tried Windows 8.
If this is happening consistently with calibre, can you try closing calibre and then using Windows to eject the device? There shouldn't be a difference, but maybe something has changed in Windows 8.
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