Sorry to hear you are suffering. Please say more about your pulmonary doctor. Are they associated with the Bronchiectasis and NTM Care Center Network? To check you can search here.
https://www.bronchiectasisandntminitiative.org/Find-Care/Care-Center-Network/General-Information
Personally, I have never heard of a BE pulmonologist say to stop with airway clearance especially when you're dealing with an exacerbation. That's the time to step up not decrease or stop airway clearance.

Last December I developed a cold (after years of being cold virus free thanks to the pandemic and masking). At that time, I had a difficult time bringing up sputum, and I skipped a few treatments here and there. Big mistake. The cold went to my chest and I developed a pneumonia.

I understand that the nebulizer treatments may hurt your throat, especially with 7% saline. Have you tried sipping some herbal tea or hot/warm water with honey while nebulizing and taking frequent breaks?

The last thing I'll say is that if you feel the doxycycline is not doing the trick for the strep throat, be sure to speak up to your doctor. I hope you feel better soon.