I have a 2008 Duramax and had a diesel shop install EFI live and pull off the DPF. I did this at about 30k miles. The truck now has 76k miles which most are highway. I changed the fuel filter at 69k and yesterday I got a code to replace the fuel filter. When it did this is went into what I am suspecting is called "limp mode". I took it right in and had a new filter put in. The mechanic plugged in his computer and there was a code for the fuel filter and one for the EGR. He deleted both codes and I drove off and it seemed to run fine. After 10 miles the check engine light came on and it went into limp mode again. I thought when they installed the EFI live it deleted the EGR? I have the 5 tune which as I understand gives you 20,40,60,80,110 more horse power depending on level 1-5. 5 being the 110 hp increase. Can anyone help me understand whats going on with this engine?

thanks,
Tim