I had the same experience -- wheezing after about 9 months in a trial that was studying inhaled Arikayce vs. placebo. (We don't know, and never will know, which I had.) At the time, I had a sequence of 2-3 upper respiratory viruses, and the CT done then showed extensive inflammation, so it wasn't clear where the wheezing came from. I was prescribed the prednisone taper twice within 2-3 months, and now I am on daily Breo which includes inhaled steroid. None of my docs are concerned about bone loss or increased infection risk with inhaled or short-term oral steroids as those risks are very small compared to the risks of out-of-control inflammation from infection, BE and MAC. (They are also evaluating for asthma given various signs and symptoms, but that looks unlikely at this point.) I will see the BE/MAC team and get another CT over the next 2+ weeks and we will assess these last 3 months of watch and wait while off meds for the MAC and on inhaled steroid.
I find it difficult to manage a good assessment of what is causing what, when there are so many variables with BE/MAC and related conditions!