Simples , you accept that you "lose" your warranty..
I have bought several new HD's over the last 22 years and the bikes NEVER go back to the dealer except to get a snag at their sausage sizzle haha..
I've done all my own servicing AND tuning since 1995 , and never had a warranty issue.
Over all those years I've had only 2 warranty claims , a speedo sensor on a 2000 Deuce , one paint issue on a CVO in 2014.
Both claims covered NO WORRIES despite my "own servicing" routine
Probably depends on your relationship with the dealer to a certain extent....
Maybe nowadays the MOCO have tightened up the show...but a speedo sensor and paint issues ???? How could I have "caused" those ?
I know it Improves performance but 2 into 1 just reminds me of a boy racer ricer p plater spec wogbox ...
like an Hyundai excel with a cannon exhaust...
2 into 2 all day for me..