I'm not real clear on the difference between PBP and Bulbar
ALS, but my mom had Bulbar onset
ALS and got the stomach flu when she had it. Other than the course of that bug, she never experienced any nausea. I would say it is very possible she had just contracted a bug of some sort.
It was very scary when she got it because we feared she would vomit and choke but she never actually threw up, I think she probably lacked the muscular capacity to throw up but I don't really know. We are certain she had a bug because our whole family had it before she got it despite our best efforts to stay away from her.
Does she have a suction machine? That would really really help her with the mucous she coughs up and she should also get some meds to assist with that. There are medications that will both diminish and thin the secretions.
Additionally, does she understand the function of the bipap? Wearing it for even short periods will help her feel less tired. I recommend making a list of all her troublesome sypmtoms and reviewing it her doctor. There are likely many little things that will help keep her more comfortable