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I don't think their OBD2 scan will be sophisticated enough to detect software changes but I've been wrong before. They are probably doing the scan to look for thrown engine codes and if your software changes eliminate those - you should be ok. It's been 20+ years since I had a car inspected in NJ - but at the time shops didn't do the inspections - they were performed at a large state run center. I don't recall if they sniffed the exhaust - but if they do - you'll never pass without cats.
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