The Theory of Phlogiston was discredited via the scientific method. It was in the act of replication that it got challenged. Phlogiston is an example of a theory that eventually got rejected as new facts were discovered and experimental design was critiqued, despite having about 100 years of apparent success.
Phlogiston theory was, however, useful to chemists. When it met its limits, and a better theory came along, they of course dumped it.
Apparently, the issue isn't scientific method per se, but of selfish interests who intentionally compromise experimental design and scientific debate for their own fame, glory, and gold.
The good news is that the these half-truths and lies will get in the way of someone else's research and agenda, and that same someone else will likely make a big stink of it.
Experiments confirming phlogiston were validated through replication. The theory of phlogiston was however, incorrect. That's the problem with the scientific method.