Mark,
I checked with one of our HW guys. Leaving the USB unplugged won’t work because the reset pin will end up floating instead of being pulled high.
You don’t need to unplug the USB to power the xDot externally though. You can connect your battery VDD to pin 2 of JP30 and leave JP5 connected. Your battery ground can connect to P2 or P14 on the DK.
With JP5 connected, your UARTs won’t work and you won’t be able to program the xDot, but LED1 and the IOs (P1 – P24) should still be functional.
Cheers,
Mike