If it were my child I really wouldn't abide by the idea of no PFTs because "they know they'll be low". I mean when a child goes to the doctor with a fever, do they say we are not going to take the temp because we know it will be high? That is a ridiculous stance. I'd suggest going to another doctor where they will do PFTs. They need to see what her scores are when she is well (as a baseline), and then see how she is when sick. The great thing about PFTs is often the FEV1 can detect a lung infection when the individual feels fine. My sons at times will not feel sick, but nevertheless their PFTs fall because they have a (silent) infection. I myself have one CF allele, chronic sinus infections, moderate asthma and a history of frequent respiratory infections. However, with all that, when I am sick, my PFTs do not dip like my sons' scores do. So even when I get PFTs during an infection, my FEV1 doesn't go below 90%. That is why they need to do airway clearance every day, and I do not. (I do, however, have to do daily sinus rinses with pulmozyme).
I think you really need to find a great pulmonologist who will treat the symptoms and not get so hung up on is it/isn't it CF. With my children, the head doctor at the local child CF center would not at first concede they had CF. The doctor at the adult center had no problem diagnosing them both with CF. He also sees me at the clinic, even though it is clear I don't have CF. It is well worth "shopping" around for a doctor who will actually be effective.
I agree 100% and I love your analogy. We weren't seeing our regular pulmonologist the days they didn't do PFTs b/c she was on leave. They worked DD in b/c she was really sick. I didn't push the tests b/c she had vomited earlier (she always does with pneumonia).