I am not a doctor but I can offer personal experience with bronchoscopies. I have had a handful of them done to me, under light sedation for various reasons ranging from theraputic lavages (to rid me of large amounts of secretions) to getting a good look at my lung's anatomy which is what I suspect your son's pulmonologist wants to do. The procedure itself is relatively quick, I recovered quickly with only a slight irritation to my lungs as a result.
Bronchiomalacia is narrowing of the airways do to floppy or softening of airway walls..this can be visualized via a bronchoscope. I know that surgery can be performed to help correct this.
I hope this helps...Sunny