Electrical problem
 

I have a 98.5 24v cummins and I'm having a problem with my gauges not working... I left my lights on on accident and when I charged my batteries back up to start all gauges did not work except RPM gauge ... So I checked all fuses (all good)... Checked batteries and one was bad so I went and bought two brand new batteries and still nothing.... Checked all the wiring and connections (all good)... Hooked my scanner to it and says (no link) so I know now that I have no link from my PCM to the cab.... So will flashing my PCM fix it or is there something else I can do??