Not sure if I follow you equipment, but I had a similar issue just yesterday (4/18/15) while 100 miles into a 300 mile ride.
2013 CVO Road Glide, with standard H/K head unit, Hawg Wired amp and speakers up front and stock Boom Audio amp and speakers in the saddle bag lids.
Without warning, the volume reduced by about 80% and the sound that was coming out (front and rear) sounded like it was in a tin can. About 10 minutes later, no sound. The display on the head unit worked, but no sound. I toggled between iPod, and radio and there was no sound.
This morning, I go to fire it up and I have sound. I put it in gear, make it about 100 meters and my sound dropped by about 80% again. Drove straight to the dealer (still under factory warranty). While there, the volume would increase, decrease and drop completely with no one touching the bike.
Hopefully, as it'd under warranty the H/U will be replaced. I imagine the dealer will find a way to balk. If so, I know there are a ton of options, but are there aftermarket units that will keep all my hand controls, to include the integrated iPod?