Hi there, my DS1 had really bad smelling gas as well. It was so surprising to me as both my DD and he were EBF and hers never smelled like that. I was told it was normal though, and he didn't have reflux or any intolerances, to the best of my knowledge.
However, since her poops have changed, I think it's worth looking into. It could be the reflux meds that have caused a change, it could be too much foremilk, it could be an intolerance, or it could be nothing. Might be worth a call to her doctor.