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It depends a lot on why you want your bike re-flashed. If it's because there's some problem (backfiring or whatever) then they likely will do it for free under warranty. Otherwise, it's probably going to cost you.
Then again, if you bought your aftermarket exhaust from your dealer they would probably be more willing to re-flash on the cheap.
An hour to re-flash is ridiculous, but most shops have a minimum. Mine is 1/2 hour but if you ask your dealership they probably have a 1 hour minimum.
Many aftermarket exhaust manufactures for the 05 S3 are reporting that they work just fine with the factory map, so I wouldn't worry about it unless there are problems; in which case you might be able to talk them into a free or reduced price re-map.
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