There are a lot of different kinds of rot as well- crown rot being the most recognizable. I don't want to sound pessimistic, so the optimistic thing to say is that there are ways that lilies protect themselves from rot & fungus. Kind of like a human adaptive immune system, it can't be reduced to NPK. Good dirt, good water quality, good sunlight, enough (not too much) fertilizer, micro-nutrients, etc.
Which brings the question- Why the rot? Can you describe it? Is there a waterfall nearby?