Seems possible that the primal grounds escape the Reset. The Church needs to have a means to pass at least intel to its next version, however that might look. They knew that there were Saints of the End before and soemone figured out that 5 additional over-fiends appeared.
If they can cheat the Reset it's another hint that they were set up by whoever came up with this shitty idea. Easiest way to enforce long-term reliance is to set up a religious organization and push the Reset button everytime someone can figure out everyone was fooled.