I don't think they will, unless you are taking it in for something like the fender liner falling apart. It's so hard to call, there's been a few ridiculous stories about dealers, but that will be fine.
They'd have to be a REAL dick to do that. Generally dealers don't give a crap unless it's something more than a couple hundred bucks, and the mod you did actually caused the problem (i.e. chip damaging an ECU or turbo, oiled aftermarket intake causing MAF to fail, etc.)
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