"The problem with a non-replicable study is that the rest of science can't build on it."

This isn't true at all. You could have future experiments set out to prove the opposite, or to dig into what novel and confounding variables are at play causing conflicting results. The fact that you have studies that inconsistently replicate is actually a sign of possible new knowledge if you can find out which undiscovered variable is causing the conflicts. Especially in medicine, you can have a case study that leads to future studies even though that specific case may not be able to be consistently replicated in other n=1 populations.

"e.g., if someone studies whether or not substance X kills bacteria Y, and it turns out not to reproduce very well, the lack of reproducibility does fairly strongly establish it can't be that lethal"

Or there's another factor that hasn't been discovered, such as back in the day before understanding gram positive and negative bacteria was even a thing. If you don't know the subtypes exist, you would see inconsistent results as that is an undiscovered variable that you can't possible account for until it's discovered. Once discovered and controlled for, the substance could be very lethal.