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It will turn the check engine light on, but the code can be deleted through programming or there is a resistor(I forget the ohm rating) that can be put inline to make the computer think it is still there.
The benefits of eliminating it are really minimal as far as performance goes. For the most part is it just a few LBS out of the car since the EGR doesn't open in low vacuum(WOT) situations anyway.
-Tim
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