Most dealers would never know if you've had a tune unless they're looking for it. If they did decide to look for it, they would know - even if you flashed it back to stock.
I've gone back and forth on it myself. I'll probably get one eventually but there's always going to be that risk that you have a legitimate issue and the dealer decides it's not going to honor the warranty.
Honestly though, how ofter do you really hear of someone needing warranty work after the first year or so? It happens but it's pretty damn rare.
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