Part of the problem with major epidemics is the severe social disruption. The "Black Death" is credited with finishing off the feudal system. With roughly 1/3 of the population dying competition for labor was such that the enforcement of keeping serfs tied to the land was defunct - those landowners who survived would be willing to ignore the fact that the laborers who showed up really "belonged" to the knight a couple of castles over. Similarly towns were much more open about asking no questions if someone showed up. This is, naturally an oversimplification but still valid. In the New World the high death tolls shattered existing societies, and the survivors struggled simply to maintain a lifestyle that kept them fed. The point being that the remaining locals were far too disorganized to resist in ways their (reduced) numbers could allow. Resistance was much less effective than it could have been.
It is unclear what death percentage is needed to have this sort of crash of society, it seems obvious this number varies depending on the society whether nomadic, pastoral, urban etc. The example of the Black Death seems to show severe disruption at 30%. For this scenario if the Native Americans are going to be significantly better off versus the Europeans the following needs to happen: you need to somehow maintain decent herd immunity against the diseases that will be imported after major contact, the interval between the first contact/epidemics needs to be long enough so that you get both population rebound and reestablishment of societal order, and on second contact the inevitable epidemics are substantially smaller than OTL.
It is unclear what death percentage is needed to have this sort of crash of society, it seems obvious this number varies depending on the society whether nomadic, pastoral, urban etc. The example of the Black Death seems to show severe disruption at 30%. For this scenario if the Native Americans are going to be significantly better off versus the Europeans the following needs to happen: you need to somehow maintain decent herd immunity against the diseases that will be imported after major contact, the interval between the first contact/epidemics needs to be long enough so that you get both population rebound and reestablishment of societal order, and on second contact the inevitable epidemics are substantially smaller than OTL.