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One definition for toilet is the bathroom fixture you pee in, which is probably why you are flabbergasted, and most likely has nothing to do with the phrase pulmonary toilet.
Another definition for toilet, according to dictionary.com, is "the act or process of dressing or grooming oneself." Although that definition isn't listed as archaic, it certainly isn't used much any more. However, my guess would be that is where the "toilet" in "pulmonary toilet" comes into play. So, anything to groom/care for the lungs would count. In addition to what TazziRN told you, I was also taught that turning and suctioning (if applicable) were part of pulmonary toilet.
The word "toilet" came to be used in English along with other French fashions (first noted 1681). It originally referred to the whole complex of operations of hairdressing and body care that centered at a dressing table covered to the floor with cloth (toile) and lace, on which stood a mirror, which might also be draped in lace: the ensemble was a toilette.
Pulmonary Toileting usually includes chest p.t. and nebulizer treatments as well. Pt's who have congested lungs from bilateral pneumonia or other lung problems that are not responding are usually ordered "agressive" pulmonary toilet.