This whole thing is bizarre. Having had a normal methacholine challenge within the prescribed time frame should have answered the question regarding asthma. A negative challenge is quite good at excluding asthma, but positive test can be caused by a recent infection, as you've demonstrated. In my anecdotal experience, COVID seems to be especially likely to cause residual lung abnormalities long after the clinical infection has resolved, which should invalidate the results of methacholine challenge. NAMI doubling down on their position is also strange. Makes me wonder if something else is going on down there behind the curtain. They're going to have to get this sorted out, since there are going to a metric crap ton of positive methacholine challenges in the months and years to come as a consequence of the pandemic.
Keep us posted on this if you can.
V/R