It's not going to harm anything at all other than your EGR being inoperative. The exhaust that comes out of the hole goes throught the metal tube to the EGR vacuum solenoid, which isn't always open anyway, so in your case, it will be like the EGR solenoid is always closed. Have you thought about the fact that the lack of EGR may be hurting your cold-start performance? I guess it shouldn't, though, since EGR should only be operating once the engine is warm. Just a thought....
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