The children sometimes forgot their religion after a long time of practicing a different religion. They also went through the stress of switching to a different religion when they were already in a new environment.
The children at the Indian boarding schools were taught Christianity instead of their native religion. they were forced to pray and go to church services even though they did not believe in that religion.
The children at the Indian Boarding schools learned Christianity. Even though it is bad that they were forced to not practice their religion, it gives them an opportunity to switch to a different religion where in the reservations they might not have the chance.