What happens if you remove the TIU from the circuit and power up? The locos should come up in conventional. I have had too many track shorts over the last almost 20 years that I've been running DCS, and haven't had one blow a board yet.
Is there voltage on the track? A short could have blown fuses in the TIU. There are no fuses in the locos, and besides, a track short will not cause excessive amperage through locos that are in parallel with the short.