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I havent heard of this happening, however it really is up to the tech. They basically have the right to decline repairs on a car with aftermarket mods and can flag the car. However if u just bring it in for those things and u have a re-flash, it will be pretty hard to detect a u have a tune on the car. So the worst thing that can happen is they program ur car and u lose ur tune. But thats an easy fix, just get it re-flashed again.
Just make sure its not ur tune causing the problem for sure before u take it in. Because if they cant fix it and the car is doing weird stuff, then they will investigate more and could find out ur flashed. Then u pay for the consequences and say ba bye to warranty.
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