Typical over-reaction to having their hands slapped by the EPA for previous illegal activity by the MoCo and it's dealers. And it isn't new rules, it is old rules that the EPA has finally decided to enforce. Tampering with emission controlled vehicles has always been illegal since the standards were first put in place.
No matter what Harley or the dealers tell you, it is still your bike and you can pretty much do whatever you want to it. As Greg noted earlier in this thread, they can't legally do a blanket voiding of everyone's warranty just because they changed mufflers. Federal warranty law is still in effect and each case has to be decided on it's particular facts and merit. For example, if your oil pump fails that can't be reasonably blamed on a non-stock muffler.
Smart people will make sure to keep any parts they replace, such as exhaust components, so they can put the bike back to stock if they have a failure that Harley might try to blame on those pipes. The same goes for tunes. Use a system that will allow you to save the stock tune and reinstall it if and when you want. Put your stock pipes back on the bike, reinstall the stock tune, then call the dealer to tow your blown bike in for some warranty work. It's a lot more work that way, but it's doable.
Jerry