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.
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