The dreaded P0401

I recently bought a used 2012 Prius and everything was working great until the EGR code went off, I talked with the last owner and the car has recently had the EGR replaced, and a little bit before that the intake manifold. I opened up everything in the car today and the intake and EGR were really quite clean, there was some buildup on the intake valves to the engine and cleaned those up some but I am still mystified why the error code and check engine light is still happening. Is there something else that could cause the code? Maybe a sensor that could be bad? I'm relatively new to working on cars and very new to Prius so any help would be great.

 

I'm getting the code for the EGR valve and replacing hybrid battery pack as permanent codes, does this mean they are actual issues? Or are these more of the things to look out for since it's a Gen 3 Prius? Both the EGR valve, intake manifold, and hybrid battery have been replaced so I'm not sure what to make of this.