IF a tune is developed correctly, it won't be an issue !!
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As long as they haven't started checking this yet, CVN (aka checksum) and CAL-ID, will be OK. Jersey has not so far, but I've also heard NY will start soon (maybe only NYC area).
Problem I see is even if you have "CARB" approved tune, will they have the new CVN's in the emission equipment, or will they send you to some ref, that will go over the entire rest of the car (just in case).