What happens to the warranty on the bike if you put the Fullsac pipe on and have it tuned?
Since HD dealerships have Dyno machines, sell aftermarket headers and mufflers (which they encourage you to buy), and sell tuning devices, it would be kind of hard for them to deny warranty coverage on something that probably 70-80% of their customers do to their bikes. If you replaced the ECM with somebody elses version, it could get a little more sticky. Basically, the burden of proof is on HD to prove that any modification to the bike was a direct cause of whatever failure occurs. Even back in '07, when they were having so many problems with the 110" engines, I don't recall them ever denying warranty work due to pipes and a tune.
In fact, a valid argument could be made that by doing pipes and a tune, it makes the engine MORE reliable. They know that. But, they have to meet EPA standards, so the bike comes stock the way it is. By altering the pipes and getting it tuned, you're definitely in violation of emmision standards though, but I don't know of a state that does sniff tests on motorcycles.
But, I'm not going to tell you that HD couldn't deny warranty coverage...I just can't recall them ever doing so to anyone on this site.