Have you tried postural drainage for your lungs? I ask because if you've lost half your lung capacity (and I expect a singer and flute player would know), then you must have some kind of junk in there.

For those not familiar with the term: You position yourself with your head a foot lower than your hips (and your back straight). You hold that for 15 minutes or so. You let gravity pull the junk out of your lungs down to where you can cough it out. Warning: It's not fun. First, your head feels like it's going to explode from the lung pressure. Second, when a chunk comes out, oxygen starts hitting an area of your lungs for the first time in maybe months. That hurts. (Or so my daughter says. She had to do this.)