I have a city with Aura of Vitality, a blacksmith, the aura that gives +3 levels, and tons (15) essence, but it only produced vanilla units *after (this may be a coincidence) a quest broke*.

I was able to churn out ridiculously powerful units before, now all my units that get created from that city were as if the city had no buildings or enchantments. I noticed this after (again, this might be a coincidence) the 'identical villages' quest broke, where I was able to defeat the Fallen in the identical village but when I return to the original village, nothing happens except the 'door closing' sound plays. The village stays on the map and on my quest log.