An exhaust or intake usually won't void your warranty except for directly related parts. Even if you have some engine or transmission problems, just put stock back on.
They can easily say that the intake/exhaust messed with the ECU, engine, or transmission by increasing power or changing fuel ratios which those may not have been designed for. Realistically, this usually won't be what messes a part up. Best to ask your dealer. Mine had no issues with intake and exhaust.
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