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You will have to block them off and have them deleted form your PCM.
Pretty much sums it up. Depending on what year you car is the air pump and egr will be different. There are tons of threads on what to do in the search section.
these are the AIR hoses. if your headers are offroad and has no egr or air hoses, you have to remove the air pump and its hoses or leave it there and delete it from your pcm by hp tunners so that it wont set your ses light.