Djoe:
I have the same issue with an Arduino nano project which is powered by a battery. The USB is not working when the nano board is powered by the battery. When I unplug the Nano board the USB is working fine. I don't think that the nano has smoked. If the FTDI is smoked it shouldn't work in any case.
Not sure what you are describing here. The Nano is essentially a miniature version of the Duemilanove. It is true that if the FT232 chip was damaged it would not download sketches, but when you say "When I unplug the Nano board the USB is working fine", exactly what do you mean?