This is an issue with the EGR vavles. First you have to verify the correct EGR valve, they look identical but are different. The problem with setting a code with dual or changed free flowing exhaust is when the ECM runs the test? It does not pass because of guidelines it needs to fall into to pass.
There are some Chip Tuners that will just turn off the light or even turn off the EGR system, both are bad choices. I worked on this for quite awhile because no one had put any time into how to change parameters of what an EGR does as they usually just remove it. But I found the EGR error 32 test and can change the passing parameters which in this case is a difference of MAP kpa when the test is run. With free flowing exhaust there is not enough change in MAP kpa for test to pass.
Before you get involved in a chip change make sure the EGR valve you installed is correct. We have found the same EGR valve in two different part number boxs. I'm leaning toward an issue like this because you have not mentioned the error 32 coming up until the valve actually failed. Did it ever work with the new exhaust?