I would ask to see an ENT. If she has a sinus infection- and you can't always tell by a stuffy nose, etc. -sometimes there are almost no symptoms, or you -or she- may not notice the symptoms because they come on so gradually- then she would have the coughing while laying down at night, <i>and</i> she could be reinfecting her lungs. Sinus infections can often improve, but not totally resolve, with oral or iv meds. Sinus rinses have helped me greatly. Also, ask about acid reflux. That can get worse when you lay down, and can also affect her lungs.
Also, have you had her allergy tested? Perhaps you have introduced something new into your home that hasn't occurred to you? I was surprised with finding out I had a feather allergy, and I was sleeping under a goosedown comforter. When it went, I improved. She may also have developed an allergy over time- it's worth checking out. Every little bit helps! Allergies= inflamation, inflamation= trapped garbage in the lungs from narrowed airways, which= more infections (at least for me).
And lastly, I would definitely ask about hypertonic saline. If she has tried the 7% (Hypersal) and she didn't tolerate it well, ask about trying 3% instead. The first 2 or 3 weeks were absolutely NO FUN, and I didn't want to keep going with it (just the awful coughing, I didn't have a bad shortness of breath reaction), but I did, got a bunch of garbage out, and I stay soooo much healthier with it.
I think that's everything I thought of to post. I hope you find a solution to this roller coaster you are on now very soon.
I take that back, are they not doing a culture everytime she goes on IV's to find out what's growing in there? That would be the first thing I would want if they aren't! They could just be knocking the infection down, but not far enough, if they aren't using the most appropriate meds for what she has in her lungs.