When your truck is under Derated, you have to do the following step by FCAR truck scanner if there is not physical part failure:
1) Go Diesel Engine, select Cummins, it will show couple DPF/DEF/Aftertream related codes. This is Hardcodes, it wouldn't be able to remove by scanner
2) Under Cummins main menui, selction Action Test to find Forced Regen Option to start Forced Regen
3) If you are installing new Aftertreatment particular filter, you will need to select Aftertreatment Installation, you will be able to find the function under Cummins ->Special Function -> Advanced ECM data ->Aftertreament installtion
4) Or if you are not installing new particular filter, you might just do aftertreatment reset
5) Final step, go back to remove codes, it should be able to reset all derate codes and the vehicle should be able to get rid of derate.