Erika,
I am certain you are sick with concern and in no way do I want to suggest anything as substitute for evaluation by a medical professional, but I did want to share what happened to my husband and what has worked for now.
My husband struggles with the the cough and secretIons periodically. Back in September we had an ER trip because of a sudden onset cough from what appeared to be a cold. There was little the hospital was able to do, but it did seem that moving him via ambulance, using the hospital suction and general jostling around helped clear him up a bit and with consultation from the doc we worked out a cocktail that has worked. Like you, I was constantly worried about his lungs and pneumonia, but although the coughing episodes have recurred several times, his lungs are clear and the nurse and docs say that the mucous is primarily in his throat, low but not in his lungs.
The key was to minimize the secretions. We use a combination of otc decongestant, cough medicine with only guaifenesin, transdermal patch and prescription pill to reduce secretions, Ativan when the cough episodes increase and the esophageal spasms ramp up, positioning in a recliner and adjusting the settings on the bipap as needed and of course the cough assist.
I say all this only because when I started discussing the problem of coughing up the secretions specifically with the ER doc, he was able to assess thoughtfully talk with us about some otc options and then give us some sound advice and guidance to help get these episodes under control. Also when working with the respiratory therapist to adjust the bipap settings. It's really helpful if she can say things like .... ' I need a deeper, shallower, slower, or faster breath.' Additionally, I have found that our ALS clinic neurologist is great about speaking to our local docs and talking them through some possible alternatives. I would put a call in to your ALS clinic and see if they have some ideas too and who they might be able to talk to where your mom is visiting.
Don't panic, and I know because the loss of voice and how bad the cough sounds, it is easy to do. Hopefully you will be able to get the coughing episodes under control and she will be able to rest and recover and return home soon.
Thinking of you,
Tracy