Disconnecting the reader can only damage files if there is a write process going on. But right beside the "Reader" lable in Sonys library, there's an eject button. Press on that and it should be safe to disconnect the reader. If you go with the "safely remove usb device" in windows, you'll have to eject 2 drives as the installer for the library is located on an additional partition of the readers memory (so it shows up as an additional hdd in explorer).
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