If USB VBUS is used to power the chip, what voltages can be present when the USB cable is unplugged?

When the USB cable is unplugged, any voltage present on the I/O pins will back-feed the FTDI chip through its protection diodes and partially power it.  This is an unknown state.  Damage will not occur; however, the RESET# input will need driven with a low pulse in order to recover.  To avoid this scenario, ensure that the I/O voltages are kept at zero while the USB cable is not connected, or use external buffers that allow signals without power present.