No that should not affect it. As long as they don't change the whim or CarPlay settings you should be fine!I just received mine and I can confirm my 2020 now has apple car play. No voice activation obviously, but only wanted car play for using google maps on my phone. I have no intention of answering phone calls or texts when I am riding, as that is my escape to begin with.
One quick question I hoped you might know the answer to... If I have to flash my system can a new flash cause this to be disabled? I added a tour pak to my Road Glide and ran a wiring harness for the rear speakers; but need to have my stock radio flashed to allow the fader to work for the rear speakers. I hope that the dealer cant somehow disable the car play if they see it.