There are two issues related to this, the first is that the virtual XInput controller stays connected when the device in unplugged and will not disconnect until Xb2XInput is exited.
The second issue is that sometimes (not sure what exactly causes this), even when Xb2XInput is exited, the virtual controller stays connected, then when you start Xb2XInput again and reconnect the controller, it adds another XInput controller to windows and these extra "ghost" controllers won't be removed until you uninstall them in Device Manager or restart Windows, the "Scan for hardware changes" option does nothing in this case.