On the Arduino Fio, the USB connector is only for powering and charging the battery, it can't be used for communication, so that was never an option in the first place.
But I just realized that the FTDI supplies power too. Even when the power switch on the Fio is off, if the FTDI is connected, the power diode is on. So having the FTDI connected would also contribute with some power to the device, and thus decrease the energy consumed from the battery, right?
Maybe I could make a custom connector which connected the five pins (GND, AREV, RX1, TX0, DTR) but did not connect the 3V3. Would such a thing work?