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The people of Magical Almost-Earth needed the Chosen One to be brought from our world. Now that the day has been saved, Chosen One would have liked to stay, marry some royal sibling and enjoy life in a whimsical world where magic exists and people are grateful to have been saved.

Alas, this was not to be: something in Almost-Earth makes it uninhabitable for Earth humans. Maybe some isotopes are different, or the chirality of some molecules is inverted, or some physical constant is different?

Whatever it is, it slowly causes health problems that will result with death unless brought back to Earth. Symptoms should ideally become significant after a few years, but not yet irreversible if Chosen One returns to Earth at that point.

What could cause slow but inevitable and ultimately lethal health problems to a normal Earth human in this world?

Magic exists (part of the world's charm), but is out of scope in this question. Simply consider it as another type of technology in this context. Local medical science is in effect as advanced as ours: if we don't know how to prevent it, neither can they. They cannot sort isotopes or similarly high-tech, extremely expensive operations of the kind.

Earth is basically inaccessible, apart from a one-time round-trip for taking Chosen from (and back to) Earth. So they cannot simply, say, grab special food once a week from Earth to solve a particular health problem.

Similarly, local environment and ecosystem are similar enough for a human to survive without problems until those symptoms start. Some fauna and flora can even be shared or closely related. And the cause should not be obvious to an average human with higher education, until symptoms are starting. (It can be obvious to a specialist, with Chosen One simply not being specialist in this particular field.)

It must also be one-way only: Chosen One doesn't cause significant health problems to the inhabitants of Almost-Earth (though draconian quarantine and the local equivalent to vaccines and decontamination were applied to avoid a plague apocalypse).

Several Options:

Ionizing Radiation: Maybe the magic gives it off. Maybe the rocks do. But it's such a small amount that you don't get ARS (Acute Radiation Syndrome). Over time, however, you start to have problems. Long-term exposure to ionizing radiation, even at doses too low to produce any symptoms of radiation sickness, can induce genetic mutations and cancer. This is the biggest risk facing survivors of the Fukushima disaster—the accident emitted a fraction of the radioactive material released at Chernobyl. But the most recent estimates predict the fallout may still cause more than a thousand deaths from cancer. If you were living in a constant Fukushima you'd be playing cancer roulette every day--and the only way to get out of it would be to seek treatment on earth.

I'm not sure why almost-humans would survive--maybe their cell organization is like a ginkgo or their magicalness protects them in some way (I mean, it is energy), but that is definitely a reason why you'd want to go back to earth.

Heavy Metal Contamination: If your world's rocks had a high content of lead, then so would the water. Much like the Flint Water Crisis, that water would be something you did not want to drink. There are species that are unbothered by such things--like your hypothetical almost-humans--but the standard earth human isn't one of them. Sure you could filter your water, drink only bottled stuff, but eventually it would still get to you because it's also in the crops, the dust, the very air... Lead poisoning isn't fun.

Not The Right Stuff: All ideas so far have been things added to the environment, what about things that have been taken away. Humans require a lot of compounds to survive, and so do plants. Nitrogen (N)
Potassium (K)
Phosphorus (P)
Calcium (Ca)
Magnesium (Mg)
Sulphur (S)
Iron (Fe)
Manganese (Mn)
Copper (Cu)
Zinc (Zn)
Molybdate (Mo)
Boron (B)
Chlorine (Cl)
are all necessary to life. (in small amounts for some of them) Maybe the plants on this world don't need Potassium to survive. The humans don't either. You do, however, and after a while you're going to have a problem there because the food isn't healthy for you. If Potassium or one of the other listed things was really hard to get, you'd run into a bit of a problem once you'd run through your natural stores.

Blue Blood: Along the same lines as the last option. If your almost-humans had hemocyanin instead of hemoglobin in their blood, then they would need a lot less iron and a lot more copper to survive. Basically the numbers for Iron and Copper in your diet would be switched.

Unfortunately for the chosen one, eating too much copper is a Problem, because it's toxic to regular humans in high amounts, so finding food would be a hassle (assumably the livestock are hemocyanin based as well, and the plants have their levels adjusted--this would be a change across the full ecosystem.) They'd also run into the problem of you being ridiculously anemic all the time, which isn't something anyone needs. Copper poison and anemia would definitely necessitate a trip to an earth hospital (and grocery store)

Disease Biome: Different planets, different diseases. Presumably all the health services on planet Magic are based off of magic. But maybe it doesn't work on us regular earth muggles, so your Chosen One can't get the proper vaccines, and has no access to any kind of medicine. No antibacterial medicine or vaccines means that poor Chosen One person needs to go home and take a sick day.

Cheers, and there's definitely more, but I think adding X toxin to the air so Y happens has already been covered quite well. Have fun writing.

You're going to have to induce a minor biological change to almost-humans on almost Earth. Sure, hypothetically, it could just be a disease unique to almost-Earth, except that it offends my senses as a writer to have your Chosen One be able to catch diseases, but not give them.

Now, if memory serves correct, carbon monoxide poisoning is pretty bad in humans. It's also irreversible, because the way it functions is that the carbon monoxide permanently bonds to the hemoglobin in your blood cells. (Irreversible in the sense there's no antidote, meaning that once you get it, you have to wait for your body to generate more blood cells. Inhaling a whiff of the stuff won't kill you.)

Almost-Earth can have a mild background level of carbon monoxide in the air, produce from some natural source (possibly a by-product of a flora-based reaction?). The natural citizens of almost-Earth have some means of countering or avoiding this (not sure how, I'd guess some system in the lungs which draws in carbon monoxide and then excretes it as a waste product). This will lead to slow carbon monoxide poisoning. The balance is tricky, to be sure, because you need the subject to build up poisoning faster than the body can replace cells, but not so fast that it kills your Chosen one in a few months.

It's not the length of time that matters, it's the date

Snodgroo flowers only bloom once every 13 years. But they're everywhere, and the all bloom all at once. For Almost-Earth residents, this means a month of severe hay-fever, and constantly cleaning all the surfaces. It's annoying at best, but not particularly dangerous.

Unfortunately, the pollen causes severe allergic reactions in Earth dwellers. Even the tiniest bit causes fatalities in minutes.

They've tried putting heroes in clean rooms before to wait it out, but the pollen really does get everywhere. Food becomes inedible and water becomes undrinkable for over year. No one is willing to risk the hero of the world when the entire world is instant death for them.

Allergens

"Almost-Earth" has something in its air that true Earth doesn't have. Maybe it's some pollen, maybe some chemical, but it is causing allergic effect in true humans, and this effect is compounded over time. There is no known remedy for this allergy, except for completely removing true humans from Almost Earth. If left untreated, allergy eventually kills true humans.

With high tech level, true human may be able to live in a bubble, but this is still risky, and what kind of life is that, after all?

Once true human returns to Earth, allergic effects are gradually dissipating until the health is completely restored.