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Your libraries will be fine. What is far more likely to be the problem is something else environmental with your PC than a reinstall though. Make sure you have no other devices of any kind (phones, iPads etc) plugged in at the same time. Try a different USB port. Try a different USB cable. Just because Windows detects the device does not mean that it is sufficiently recognisable.
For instance my Kindle (well, before I squashed it) shows up in Windows, but cannot be seen by Calibre unless my HTC phone is unplugged from USB.
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