I went in for a failed HPFP and they replaced it without saying anything about my intake and intercooler.
I went back in with complaint about turbo whine and they said they would have to charge me a fee for troubleshooting the car, but would refund the fee if the fault was not related to my mods - or - put it back to stock and no fee. I brought it back with next week with the oem intercooler and they worked on it for free.
Never heard a peep about losing my warranty. I think from their perspective they have to rule out your mods as a possible cause of an issue.
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