Could I ask for more details about the epidemiological situation?
Iirc, you "gifted" the Haudenosaunee and Wendat with a variola major outbreak. This is a highly contagious disease, so on what grounds does your assumption that the initial outbreak was contained to the warriors stand? I suppose it is because of the low population density; but wouldn't the displacements of people during the war counteract this? I would be highly surprised if not a single infected warrior didn't make it back home to spread the disease.
Indeed it is. And indeed this is a very specific type of outbreak. The settlements of the Rhagenratka were primarily along the shore of Lake Erie, the biggest cluster was around Niagara. Since the virus only infected the natives after passing there, these local villages were not affected on the voyage to Wendake.
Then when the outbreak becomes obvious in Wendake, they are deep in enemy territorry, not exactly a place where a single warrior would wander off.
When the army finally gets bogged down from disease around the Tionantati, the disease spreads to them. But, the Tionontati are still not on the best of terms with the Allies, so there is not a high chance they just send people to the south.
For the Army itself, the Wendat bands still are a threat in their minds, so they are quite careful about not wandering off. Then, in this camp, contact of course is very close and therefore the infection speed is very high. So all that will die, die very fast.
What this does, except the gender imbalance, is giving the natives an outline of the concept of a quarantine. In OTL they had the unfortunate habit of Gathering among the sick, which is.. of course suboptimal.
After over two months the remains slowly move south, and everyone of the survivors is no longer infectious when they arrive in the Rhagenratka villages.
Second, you mention the metis as immune to the disease - is it because immunity (well, at least resistance) is transmitted genetically? (I really have no clue about disease, sorry).
Okay, first things first. They are not inherently immune as in they will not contract the disease. Even in the isolated European colonies smallpox regularily killed a lit of people since the colonists had had no previous exposure and therefore aquired immunity. It only reduces the Death Rate from the near annihilation pure natives faced to a devastating plague. The effects of smallpox e.g. will still be much more severe than in Europe.
Let me explain: One of the big issues for native american in that matter is their extremely low genetic diversity. I would refer you to
this post and the conversation below to outline the problem and what a a metis population can do to mitigate that and what not. In short, it is not gonna be a wonder cure for the epidemics, but there will be a functional society left. Especially, since this measure drives down mortality from all Old World diseases, not just smallpox.
Third, I suppose after a number of waves of the same disease, the native population should be immunised in turn : how long did it historically take? Is there a chance of the population bouncing back, say, in the XVIIIth century instead of undergoing a long decline under the pressure of war, diseases, and colonisation?
OTL Mexico.
A bit what i said above. The low genetic diversity will always be an issue if you dont have populations mingling. "Immunity" as such is lost after each generation that got hit by the disease if it does not go endemic. This is not realistic in the Haudenosaunee/Neutrals since their population is too low. Another effect we may however not forget is how the natives were treated OTL. Their mistreatment and bad living conditions came with low birth rates, early deaths and high child mortality. So the still functioning metis population makes it much easier to rebound demographically. Also, given that the metis children will naturally survive in higher numbers than their peers without European influence, their DNA will become more widespread over time. Combined with the introduction of European crops like wheat through the contacts with the French, the Natives in TTL stand a much better chance of recupering from the epidemics. If one assumes, say 3/4 of the growth rate a European colony can reach, than this graph above would look completely different
Last, you mentioned you were interested in the effects the epidemics had on the survivors - any hint on cultural changes brought among the first nations by these outbreaks, OTL and TTL?
OTL the Jesuits really fell out of favor among many natives because they believed the "Blackrobes" had brought the diseases, which of course hindered attempts to convert the natives.
The Haudenosaunee went berserk with their Mourning Wars, because to them there was almost no such thing as a natural death (excluding drowing ironically). They would then attack neighboring tribes for revenge and get captives to replace the losses. Of course this would lead to more deaths. And this to more mourning wars....well, safe to say - it was not very effective.
The societal effects are proably even more devastating. But frankly, I have not found a good source on that. I figure it must be incrediblly hard to procure such information from original sources.
TTL the Jesuits will not fall victim to this mistake by the natives. However, there is nothing I can do to change the mourning wars before there is a significant portion of Christian Haudenosaunee. They will exist, they will be bloody and the Mahican, the Susquehannock and the various Algonquian Nations will suffer.