The wheezing can be made worse by the reflux. How long has she been on the Prevacid?
Realistically, I am glad your pediatrician is taking an active approach to all this especially given that it's flu season. I would keep a good eye on her and track her symptoms if you can (e.g. how many nebs she needs etc). that way you will be better able to tell if she's improving or not and if you need to get her back in.
At 9 years old my daughter got a chronic cough that we couldn't get rid of with any of the asthma meds. On a whim, having remembered research that I once read about asthma like symptoms due to reflux, I put her back on the Prevacid that she had stopped when she was 4. The coughing stopped. After 2 weeks, we stopped the Prevacid. Cough came back. Back on Prevacid, it was gone again. So, we've gotten back down to using only Zantac instead of the Prevacid but for her that's what she needed for the cough.
The fact that the nebs aren't working for the wheezing makes me think that her doc would want to look further into it. Does the wheezing get worse after she eats? Has her doc considered a swallow study to make sure she's not getting little bits of food into her lungs?
Prevacid is much stronger than the Zantac. It's also very possible that the Zantac may have needed to be a stronger dosage to be effective for your daughter. My daughter was on a very high dosage of Zantac when she was a baby. Her pediatrician would not prescribe that high but her GI doc did. It was the only way we could keep her okay. She was a baby when Prevacid was very new and rarely given to babies. My third baby on the other hand got Prevacid first.