How can a egr deleted 6.0 throw a p0403 code?

[Belize]

I have a 2006 6.0 EGR delete that has been running beautifully. This morning I started her and she ran rough for about 30 seconds, then smoothed out. The CEL came on so checked codes and there was a p0403 which points to the egr solenoid or an electrical problem with the egr system. With the egr deleted, why would I get an egr problem? The symptom also matches what a p0403 code describes. Is the solenoid still active with the egr deleted, starving a starting engine of oxygen? So what would be the best procedure to track down the rough start and p0403 code? Thanks!