Very few. The phlogiston theory of combustion proposed about 1695 was overturned after oxygen was discovered in the 1770s. The evidence for this theory was slight and in some situations the theory predicted that phlogiston had negative weight. Since few chemists actually weighed anything then, the theory survived for about 80 years since it did explain some things fairly well.
The theory of evolution by inheritance of acquired characteristics was vaguely proposed by Charles Darwin's grandfather Erasmus Darwin, and later more definitively by the French natural philosopher Lamarck. That theory did not last long as it was disproved by experiment.
The person who wrote about the flat Earth does not know what they are talking about, the Earth has been known to be round for up to 2500 years. After the year 600AD a couple of theologians proposed it was flat on Scriptural grounds, not on observation and measurement, but everybody ignored them.
If the church has said the Earth was flat when Colombus went to see Queen Isabella, she would have handed him over to the Inquistion, her favorite part of the church and not given him three ships.
The idea of the Earth being at the centre of the solar system was not a scientific theory. It was merely assumed that the Earth was the centre. But there seems to have been a Greek philosopher more than 2000 years ago who said that the Sun was the centre. But Plato said the Earth was at the centre, and the early Christians liked Plato better for other reasons so they took his word for it.
There was at least some evidence for Fred Hoyle's continuous creation theory that attempted to explain why the Universe was expanding. But Fred lost out big when the cosmic microwave background was accidentally discovered about 1965. The big bang theory predicted the microwaves, Fred's theory didn't . 'Bye, Fred.
Lots of small theories get chucked out all the time. The big theories like evolution, big bang, gravity, combustion, the atomic theory and so forth have evidence piled high wide and handsome, and there is little chance they are going to disappear. They may get modified, but that is science working.