Which ones? I don't know of settled science that has been found to be false, but maybe I just don't know.
Sometimes a new theory might eclipse another theory - cover all that ground and more, but that doesn't make the prior theory wrong in any way. My new, faster laptop doesn't mean the old one didn't work.
Phlogiston theory is post-Baconian. To me, Bacon was the first to articulate the method of thoughts that characterize good modern science: Observations, theory, prediction, experiments to verify the predictions. So I don't think saying we've thrown out pre-Baconian theories is germane to the conversation.
There is a Wikipedia page for Superseded theories in science. https://en.wikipedia.org/wiki/Superseded_theories_in_science
If that's the best you have, we agree! :)