Smallpox doesn't go away on it's own. It's been circulating in their populations on and off, for our part we've only really been infected whenever we went down there.
A citation from reality
It has been speculated that Egyptian traders brought smallpox to India during the 1st millennium BC, where it remained as an endemic human disease for at least 2000 years.
Overall, it's not leaving on it's own, it just takes a nap every so often.
Okay, so to help elaborate:
-Sacred Forest
--Sacred Forest includes a regime of deliberate reforesting of trees, performing controlled burns of diseased trees, directed harvesting of dead and live wood, as well as replenishing the soil with Black Soil(no longer needed really, by now the black soil layer is likely a meter thick)
--Tree Blight is caused by stressed trees, this depends heavily on the soil quality. As we've been replacing the soil with Black Soil, they are likely to ignore droughts for a long while even if we stop maintaining it.
--A forest without controlled burns with no deadfall harvesting, grown at orchard densities does not automatically become a firetrap. What you need is a few years of very short dry seasons and long wet seasons to build up a backlog of deadfall and debris, then followed by a drought to dry it out. Otherwise you'd only have seasonal small natural fires that burn out the leaf litter without causing lasting damage.
---This isn't happening much because we're harvesting deadfall aggressively to fuel our charcoal demands to feed our iron industry incidentally. And we've also greatly increased irrigation all over.
Why Sacred Forest might stay even if the belief is challenged and fails the challenge is our metal industry demands charcoal, our shipping industry demands fine timber, and so does our bows and chariots. Coupled to Divine Stewards, we'd likely change it to 'useful' plantations instead
But as practical qualities, tree farms for the purpose of timber is distinct from the artificially reinforced ecosystem we create, and more fragile to disasters.
-Sacred Warding
--Sacred Warding comes in two parts, the clinics to maintain the medical services, and the sacred herds we use to pass on the cowpox.
---Clinics provide improved healthcare overall, if you shut down a clinic, it will produce an uptick in minor diseases and all that just by not having people being cared for.
---Sacred herds provide a powerful ongoing supply of veal, which is a quality of life that's not really matched for the era.
--Smallpox remains endemic in the population of the lowlands, though less so in the nomads who don't meet the mmuch. How convenient then, that we can send trade missions right now to the lowlands to pick up fresh samples.
--Vaccination needs to be missed from birth to stop working entirely. How convenient then, that we just took in
refugees war-loot who aren't vaccinated, allowing us to skip a generation's wait in testing the theory.
Odds are good that we will keep parts of Sacred Warding even if the process of challenge fails. The clinics provide real and quantifiable effects to population health. The Sacred Herds produce such quantities of high quality meat that people are unlikely to want to stop even if it wasn't a religious duty.
But as practical qualities, we'd likely lose the chain of cowpox if it's not tested adequately against smallpox. Why, after all, should we relay diseases from cow to cow on purpose if it does nothing?
