Truck Repair: removing autoshift trans from 02 w900l with ISX, auto shift, ftlbs

Question
I was told by a cummins mechanic in B'ham Al. that I would have to re-program my ECM if i switched from my auto-shift 10-spd Eaton to a manual 10-spd.Is this true or would the truck run ok without re-programing.

Answer
YES because the ECM controls the top two shifts.Hehe one of my old branches of Cummins Mid South,LLC.Would be a good time to up the HP too since it will not cost anymore & I would not do the 525 because torque is lower(1590ftlbs) than a 500 HP (1650 ftlbs plus 200 extra in  top 2 gears).