Who ever said knowledge is complete? It certainly wasn’t a scientist. The ability to look at new evidence and modify old understandings of the universe to form that new evidence is a feature of science not a shortcoming. All scientific understanding is subject to modification based on new findings.
That said, it is not that easy to overturn our basic understanding of how things work. It would take a monstrous amount of work to overturn something like general relativity or quantum mechanics. These theories have made correct predictions within their domains with a one hundred percent success rate. Any challenging theory would have to make the same predictions in all situations already tested plus novel predictions for untested situations that are different from what the existing theories predict.
That’s a tall order. Basically it means that you cannot expect to revolution physics by saying “The existing theory is wrong; my alternative is right”. None of the examples you posted are likely to overthrow existing theories. As an analogy, after the discovery of the planet Uranus, one of the first things astronomers naturally did was use Newtonian gravity to calculate the orbit of the newly discovered planet and compare it to the observed position. They found to their surprise that the planet wasn’t quite following the predicted orbit. Was this the end of Newton’s Law of Gravity? Not so fast: there was a factor that was not accounted for in the calculation, namely the presence of another previously unknown planet. The astronomers calculated what the mass and orbit of such a planet must be to account for the observed deviations and worked out where to point the telescope so they could see this hypothesized planet and lo and behold, the planet Neptune was found.
I suspect something similar might be the case regarding proton structure (although I have zero expertise in particle physics). It might turn out differently though. There is another analogy from astronomy, this time regarding the planet Mercury. The point at which Mercury makes its closest approach to the sun, known as its perihelion, does not occur at the same position in its orbit on each orbital cycle, but rather processes around the orbit. That is if we call the current perihelion point zero degrees on the orbit, the next perihelion does not occur at zero degrees, but at a fraction of a degree past zero. Newtonian gravity can explain this, but this precession is greater than predicted based on Newton’s laws and the known planets. Guided by the discovery of Neptune discussed above, astronomers naturally postulated a planet closer to the sun than Mercury that would account for the discrepancy. They pointed the telescope to the calculated spot and lo and behold - nothing; no Vulcan.
Well, they were obviously very puzzled by this. They thought that it might just be very difficult to see a planet that close to the sun and that it might just be too small to image. It took an Einstein-level genius - literally- to explain it. The precession of Mercury’s perihelion turned out to be perfectly explained by General Relativity based only on the new theory and the known planets.
How many tests of Einstein’s theory of general relativity have there been?
“Who ever said knowledge is complete? It certainly wasn’t a scientist.”
Scientists probably don’t say it, they just operate like that — “my professor said it, I believe it, that settles it.”