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No problem. Just make sure you call them and talk to them about what's going on with it, and what you've done to your car. Then as a re-assurance method, attach paper showing what you have done to your car, to your ECU. This will help them better tune your ECU (It's obviously better to tune an ECU while it's still in the car, so they know exactly how to map everything) But if you can be as detailed as possible, I'm sure they'll fix it up nice.
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