Holy Farms will only be overridden and captured by the Slave Traders, functionally turning it into a slave farm, if High Inquisitor Valtena, Esata, and either Holy Lord Phoenix or High Inquisitor Seta have been killed/kidnapped, as long as Emperor Tengu and Longen are still alive and free.
Due to being incorrectly assigned the overrides of the Holy Mines, it might flip to Shek Kingdom, Kral's Chosen, or a destroyed version shortly after going to the Slave Traders, if the appropriate conditions are fulfilled. Possibly preventing the Slave Traders override from ever appearing for the player.
There are dialog changes to farmers if the Phoenix is dead, and Esata is alive and free, though this is not an override, and the farms will remain in Holy Nation control.