The answer may be in the numbers of each one present. I haven't found S.boulardii to be that effective against fungal candida. It looks great in lab experiments, but not in clinical practice. Many pathological organisms can support each other. This happens with E. coli and candida, as well as candida and other pathogens.
Candida can cause its own conversion, so it's likely that it could do it for other yeast/fungi. It depends on all the conditions present.