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I couldn't imagine it having an effect on the OBDII like that. It would be the same if you had a regular EcuTek tune. As long as codes are cleared, readiness should be fine.
Even if Vortech's mapping had codes shut off, it still wouldn't effect anything. When I had Hydra in my STi, I had an opensource tune done to my stock ecu that cleared all codes and the readiness so I could just literally plug it in and pass emissions.
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