A few thoughts on what happened
first if a batt is shorted inside (not uncommon) you can NOT charge it to full 12.5+V as a shorted CELL will not contribute to the voltage output and secondly I have a hard time believing a shorted battery killed your BCM and engine ECM
I would suspect more likely incorrect charger usage/high voltage was applied IE like a REVOLT system would cause the ECM's to be damaged
to test a battery for a short charge it with a normal battery charger until draw current drops off and or charge voltage starts to rise (depending on charger style)
and disconnect charger and check the batts VOLTAGE after one hour and should be over 12.5V and upwards of 12.8V of NOT shorted but if shorted the charging voltage/current draw will NOT rise/drop
and the standing voltage will be 10.5 to 11V range
also if it was below freezing when your truck was parked and dies the batteries may have frozen inside which will prevent the battery from accepting a charge during your initial attempt to start
first if a batt is shorted inside (not uncommon) you can NOT charge it to full 12.5+V as a shorted CELL will not contribute to the voltage output and secondly I have a hard time believing a shorted battery killed your BCM and engine ECM
I would suspect more likely incorrect charger usage/high voltage was applied IE like a REVOLT system would cause the ECM's to be damaged
to test a battery for a short charge it with a normal battery charger until draw current drops off and or charge voltage starts to rise (depending on charger style)
and disconnect charger and check the batts VOLTAGE after one hour and should be over 12.5V and upwards of 12.8V of NOT shorted but if shorted the charging voltage/current draw will NOT rise/drop
and the standing voltage will be 10.5 to 11V range
also if it was below freezing when your truck was parked and dies the batteries may have frozen inside which will prevent the battery from accepting a charge during your initial attempt to start