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There are modifications you can make that will not effect your warranty, such as air intake and some exhaust mods. Engine tuners are not among them. While tuners may not leave code remnants in the computer (assuming you remove the program prior to taking the truck to the dealer), the computer does record when a change to it has been made, which in itself leads to suspicions.
Other posters pointed out there are some dealers who will install power upgrades and still warranty the engine, but what happens if you are a thousand miles away from that dealer when something happens?
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