I can't think of one that neatly encapsulates the idea of the situational separation of the two states. To express the idea in the clunky terms I have on hand, I would say such a pathogen would be "beneficial or harmful depending on the environment/situation".
Idiomatically, it's akin to a "thorned rose" or a "blessing in disguise", but this still refers to something within a singluar circumstance, not two separate ones.
Awhile ago I invented a word for something similar, and I'm going to try a derivative of it here.
The word I made was ambiatives, meaning "of or related to both sides", implying both positives and negatives. It's meant to be a direct replacement to "pros and cons".
For this, I'm gonna use "ambificial": "ambi" from the latin for both, and "ficial" from ficus latin for "making, doing". Thus, a beneficial thing makes something good/better, and an ambificial thing can make things better or worse. (And it's all latin, so I don't feel bad gluing some roots together and calling it a day, lol).
Something situationally beneficial makes something better or neutral under the correct conditions, and something "situationally ambificial" can make things better or worse depending on circumstance.
If someone can find a better (real) word, please let me know because this is gonna bug me.