I have that Harley windshield triple pouch. To keep it from scratching the windshield, and to keep it from rattling against it, I used some black sticky back velcro (the soft side) and cut it into little squares that I stuck on the corners of each pouch between it and the windshield. No more rattling, no more scratching.

 

I will try the Velco fix. HD dealer screwed up on the install and put too long of screws on the inner fairing. Thus they have to take it off and re-paint.