The phrase "long term" means different things to different people. Obviously you know there's some elements of risk, or you wouldn't be asking. Unfortunately, no one has a "crystal ball" to reassure you that nothing bad will happen. As far as pheromones (& btw, what are their genders?), I'd try swapping them in smaller containers first (tubs or even pillow cases) to gauge their responses before going all in on the swap. Honestly, I'd prefer a deep clean w/ substrate change, but it's your call, not mine. Some people gamble, some don't.