The sound coming out of the pipes has become light and full
of air, kind of like an exhaust leak.

Anyone know what could cause changes in the exhaust sound?

I have a 2003 fatboy with open pipes.
It sounded great up until recently. Low rumble, no air.

 

Could you have had the bolts on the heads loosen up or a broken gasket there?

 

I don't think that there are any loose bolts or
leaks of any kind.
The noise only comes out of the correct end of the pipes.

It goes almost completely away after 10 miles or so.
Almost.

 

I would think from your description of a leak around the baffles that heats up and expands after a while of riding