2005 Dodge Ram computer reset

I recently failed a smog test/check due to what i'm told was because the ck engine light is on. They said it may be due to the fact that I had 2 new batteries installed last year and that caused a loss of power supply to the computer. They said the computer should have reset itself and re-establishing the battery power supply. Obviously it didn't..what can I
do so I can pass the smog check?
The truck is a 6 cyl diesel/turbo cummins.