Diagnosing exact causes of pneumonia and upper respiratory disease is difficult, slow and often not practical unless you have a large scale operation (thousands of birds). Most treatment is symptomatic as well. Stress is usually a major underlying factor (heat, cold, wet, transportation, commingling, major changes in feed or environment, old or young, overcrowding…) along with aerosol irritation (smoke, extreme cold, dust, noxious fumes…). Exposure to novel viruses from wild or strange birds is also a risk factor. Most pneumonia is actually the result of an overgrowth of pathogens already present in small numbers within the host’s sinuses or respiratory tract, but other factors have allowed the population to get out of control. The immune system then freaks out causing the major symptoms while trying to reetablish a proper balance. Some pathogens like certain mycoplasmas and herpes viruses continue to exist in an asymptomatic host and cause disease during stress (cold sores in humans). Antibiotics (broad spectrum) are often used along with anti inflammatories (No good options in quail!) to treat sick or at risk animals. Vaccination (depending on species, again not quail) is also used to stimulate an immune response. Good nutrition, ventilation and water availability as well as appropriate nursing care are vital as well. I’d guess your ladies are just getting on in years and have a weakened immune system and are more prone to infection (pneumonia is very common in old people too!). Isolating the male may or may not help, yes it will reduce his exposure but how much will the stress contribute to his own response?