This is about creating an abstract cause of conflict in your game world. One one side are the defenders of the Ancient Way and on the other side are the Newbies. And adding fuel to the fires of ambition which had been lit by the torch of desiring understanding is some approaching cataclysm. The Ancients say to go through Door A, and the Newbies decry this, and proclaim not only the virtues of Door B, but the fact that Door A will 1)Waste time and/or 2)Make things worse.
There are two types of changes in scientific theories. In one, such as the change from Newtonian to Einsteinian ways, Newton is still valid in most cases. Its only at the edges that Einstein holds sway.
In the other, such as light being carried by the ether, the whole thing is tossed out. I'm going to reccomend the second for your world you're designing. Its more clear-cut and that is a good thing for such an ethereal conflict.
Otherwise you're going to be spending more of your Imagination Budget explaining that Theory Y is mostly correct, but in this special Circumstance Theory Ya takes over. I suppose that would not be too bad, actually.
"Well, George, its like this, werewolves generally rise on the full moon, and infect those they bite but don't kill. And in order to stop them, you have to hack their heads off. But we at the Institute for Magical Transformations have discovered that when a werewolf shifts because of extreme rage during the day and injures someone, and they turn, you have to also burn the ashes because mere headchopping ends up creating two werewolves, kinda like chopping an earthworm in two. Unfortunately, those reactionary yokels at the College of Wolfen Change Studies are clinging to their century old theory and ignoring this new wave of Rage Wolves which is threatening to depopulate the Korestiv Frontier. They are afraid that King Henry the Miserly will cut their yearly grant in half and give the other half to us so they ignore th eplight of th epeasants."
So, yes, you can do this sort of thing in the right magically based worlds. If your High Mag Bias world is the sort where academicians gather to discuss the best way to create teleport spells or the most efficient method to disintegrate a master vampire, that is.
Now one would think that scientific theories die when a contravening fact shows up. This is not true. What happens is that such a fact gets labelled an 'anomaly' and in effect what happens is the Theory's supporters trundle off to the Bank of Credibility and write an IOU from the future to themselves now.
"I know this does not make sense with my theory, but polonium halos are a little mystery which will be resolved in due time." Thats your IOU.
Of course, eventually, you run out of credibility at the bank.
Unless of course, you think your theory is the end all of theories on the topic. In that case, go lay down and play soft music. Reality is disturbing, and we don't want to disturb you.
You can also do patch work to theories which is like putting patches on pants with holes in their knees which people don't do much anymore. But there are limits to this too. Occam's Razor slices such complicated forests of explanations down to size. The scientific temperment prefers the simpler and more encompassing explanation, as it seems so does Reality in general.
Theories are not just theories. They are often statements of politcs or philosophy as well. As such, it might not surprise you that the noted Geology Club that was formed to promote Darwin's new theories had not a single geologist on it. One of the groups that supported Darwin was the old aristocracy because they were on the defensive. Winds of change...capitalism, democracy, middle class power and such were blowing. And Darwin's theory admitted change all right, in fact, change was central to it. But the key point from the aristos point of view was that it was VERY Slow change. The aristoi would have been perfectly happy to have scheduled the big talk about social change in the Year Three Thousand instead of 1914.
Let's go back to our werewolves.
The Institute was founded after the preceding king built a nice, straight road to the Korestiv Frontier so that all those peasants could send corn to his growing capital city, and also more tax money. They had the worrisome habit of ignoring the king's tax collectors and upholding ancient and supposedly (according to the predjudgiced view of the city dwellers who ran the kingdom) backward and barbaric traditions. Like they yanked out the tongue of a liar instead of doing the decent thing and whipping him with a flail.
This prejudgdice served the purpose of 1)warning city dwellers that the Frontiersmen could be different and dangerous. 2)gave an excuse for city dwellers to exploit the frontier.
King Henry started the Institute because he wanted to enlighten the locals and create a local leadership class that was mostly on the same page as he was. It worked very well, with some opposition from locals who thought the 'edimiccated sorts' were snots and sell outs, but the 'edimiccated sorts' proved their loyalty to King and locals by making sure the locals got better deals and the King got his tax monies. Every one was happy except for the 'bloodsucking merchant scumbags' in the capital who had gotten used to exploiting the frontier by selling second rate stuff for top dollar.
Unfortunately, King Henry really was miserly from their point of view. He wanted his tax money, and if that meant making the merchant houses working a bit harder, it was no skin off his nose.
The economy boomed. Local Korestiv men became second-rate merchants (not nearly as wealthy as the capital, but still quite well-to-do.) Even the merchant houses in teh capital did well, but they lost status. Now they were merely primus inter pares instead of the only dog in the hunt.
And then someone came out of the forrest. Its not true as some of teh more suspicious minded of the frontiersmen think that the city merchants summoned it. They are not that black-hearted, nor that visionary. But it was the first conscious of his power Rage Wolf. And he deliberately began to create a kingdom of Rage Wolves. This attracted other normal werewolves which he did not mind, but he did not tell them the secret of his power which he kept to his 'children' who were as werewolves are loyal to their 'sire'. Because he intended when the power struggle for dominance over the new wolf kingdom came to be holding the high cards despite what seemed like other more powerful werewolves joining him.
This split of Rage and normal werewolves fuels the case made by the College.
The College is older, and its done good things. Its supported by the city merchants now just as the rising merchants of the frontier support their old alma mater, the Institute.
The College resorts to all types of logical fallacies and tricks. One of its favorites is 'do you believe a genuine master of the occult arts, or a peasant?' The college also refuses to debate on the frontier 'we don't want to waste the king's time. You can come to the court of the king.' And then they arrange all sorts of small tricks to weaken the speaker for the other side such as dousing the candles near him with elemental water so they won't light, and arranging for someone with the croup to sit near him, and giving him a pitcher of water with a crack in it. They also ask for one speaker to be sent, and then show up wth five speakers for their side. And a speaker who arrives a day early must be cautious as he has a far higher than normal chance to be robbed, pickpocketed, accused falsely of a minor crime, or challenged to a duel than is normal.
The College proclaims itself a bastion of fair debate. There are two problems with this. 1) Its fair to those who are Important aka In the Club. Peasants are not important. In the club its 'my honored opponent should perhaps look at things another way...'; outside the club its 'this doltish fool with his simpleminded superstitions needs to be arrested for makiing a public nuisance not answered with an unearned respect accorded to true scholars.' 2)True decadence has set in. The College used to have robust debates inside the club. Now its more of 'flava of the month' and 'whatever the chairman thinks is wise is wise.' They still claim the title of robust debate, but no one debates because everyone thinks the same way. Intellectual inquiry is more along the lines of 'how can those simpletons think that way?' in reference to the Institute.
Now, teh College is aware of Rage Wolves, but they are also aware that sending big bundles of cash to the Institute would hurt them directly, and that the necessary movement of the Royal Army to protect the Frontier would 1)drain the coffers of the city with a war tax. 2)stop weakening the frontier back to subservience. 3)probably strengthen the frontier as a lot of the city's war tax got spent on local to the frontier forts and food and stuff. The Frontier does not see this because they are focused on 1)The damage done. 2)the great cost of tax on themselves (it will be a flat tax which means the city will pay more in pure numbers, but all will hurt) 3)the likely result of war and looting in their homes as soldieers are not the best neighbours in a war.
So the College works very hard to paint the Rage Wolves as an anomaly, or come up with a patch. There are also a number of brilliant young theorists of the city who are trying to come up with a brand new theory which will support the College, but at the same time be more accurate.
This is another case of what happens when political need and science meets. The old theory is bad. The new theory is correct or so it seems, but it hurts those with the power. So what is desperately wanted by those with the power is a theory which will let them keep on, keeping on and be accurate enough. In the meantime, the power will protect the old theory as hard as necessary while searching for a new theory it likes. If it finds a new theory it will dump the old one super quick and jump to the new one.
And this is a point about Free Enterprise and Government. A bad idea generally goes bankrupt. A bad idea supported by the government might require a total invasion and destruction of that government for the accounts to be balanced and reality to be asserted. But in the end, Reality is more powerful than a Lie.