EGR Code delete using torque pro

now I had read somewhere that the app has the functionality of being able to turn codes off so they wouldn't be popping up for rear cat and egr

so after installing SD headers and doing an egr delete I fired car up idled rough for about half a minute and evened out I dont have the pipe that would take place of cat installed yet as I need a new flange welded on I wanted to clear my ses light before heading out and was able to reset the codes by clearing but it did not stop it from popping back up after restarting car

if this is something i'm going to have to have a tuner do thats fine if anyone else has any exp with this and could steer me towards a resource or method I would greatly appreciate it

Tuner only.

thanx