We do not have schematics publically available for the Expansionboard 3, though I'm not completely sure what is/ is not working for you.
You mention powering the Fipy directly in the expansionboard using the Vin header (right next to the battery connector i presume) with 3.3V? Then, you attached the USB cable, and the expansionboard got damaged?
Could you verify the Fipy is receiving power on Vin, and generating 3.3V on the output, using the presumably broken expansionboard with a multimeter (of course without attaching the separate 3.3V supply).
The mosfet you encircled is, if memory serves me correctly, the power switching mosfet, switching the power source between battery and USB, depending on which is connected, perhaps explaining why it is broken, as the 3.3V was backfeeding, though I would expect the USB voltage to overpower your 3.3V source.
You also mention you're able to flash the PIC, does it then also show up on your computer as a COM port? Could you also let me know of the voltage on the Vin pin without the Fipy present?
There is no way to disable USB power going to the Fipy, without doing some physical damage to the board (ie, remove one of the components or scratching a trace).