I think that’s a really hard and sad situation!!!
Is this person familiar with the gospels? If not could you get him a Bible as a gift and encourage him to at least read it? Letting him know that Our GOD who had everything, needed nothing but that He loved us so much He became a man. He lived with lonliness, poverty, sorrows, humiliations,and suffered a horrendous death for the love of us and because He wanted to be an example for us to live by.
He never promised that living in this world would be without suffering or persecutions but He promised that those who endure it will have eternal peace.
Could you tell him that even though you don’t have the answers as to why he had to suffer so much as a child he wasn’t abandoned and God grieved and hurt right along with him. The psalms could be helpful to him also!
(I love Psalm 139)
God understands his sufferings because He, himself, suffered at the very hands of those He created.
I don’t know if something on the lines of what I just said would be helpful or not but at least he would know that even God wasn’t without suffering.
I hope everything works out and I’ve said a prayer for the atheist. May he find God’s peace.