Hey there Sis, I felt your words and I personally don't have words to express a solution to your pain, but I consulted a friend of mine who is also a parent and she has given me these words. I hope they can give some comfort.
She writes, "My first thought is that she must be willing to take the knocks with him as he grows up. It is completely unreasonable to expect a child to appear to be perfect all the way through their childhood and into adulthood. They will fail with temptation many a time, as we all do. Unconditional love is worth a great deal to their ongoing relationship.
Children absord things we would rather they didn't, as well as them rejecting things we want them to accept. Being a parent is very challenging, and is best done from the shelter of God's hand, and under His direction. She can 'do' only so much, and then commend him to her heavenly Father for the ultimate sanctions.
My second thought is that if he's been smoking and drinking, the depression which goes along with trying to break an addiction can be very deep and extreme, and recur even in good times - when a person has let down their guard. I would say she needs to pray for healing for both the damage done by the addictive experience psychologically, and healing of the body affected by the addctions.
She needs to assume that he is battling with suicidal thoughts, but not question him about this. Conversations must not lead in that direction as if it may be a solution to the difficulties of life. Young men have a strong 'doing it' drive (whatever 'it' is), and if she can keep him moving towards and through positive life experiences, they will begin to fill the void he feels.
I would wonder if maybe he's been exposed to pornography during this rebellion, which is both depressing at that age, and deeply disturbing. I don't know what kind of health education he might be getting formally through school, but my impression is that most adults have no idea where the boundaries are about what a child needs to know about sex, and that children themselves are confused. Photographs are damaging psychologically, compared with mere biological information conveyed by drawings and the spoken word. If he has this kind of thing on his conscience, she doesn't need to know what is troubling him still, but she needs to talk to him about the fact that God created everything to be enjoyed in a functional way and according to His prescribed boundaries (Maker's instructions), and it is 'sin' to pervert His designs. Repentance is required, and a desire to do things God's way, and to become a person that sees these things from God's point of view. This is true maturity if he can aim for it.
Going to church is not as important as him developing a meaningful prayer lfe first, and, learning to read the Bible in a non-religious way. That is, that he should begin to learn how to look for God's character in the narrative, so that he gets a theoretical grasp of how God deals with people, including His mercy and grace to the repentant, obedient, honest seeker for a relationship with the Lord. It is the Lord Himself who has to become the focus. I would recommend she start looking for interesting Chrisitan biographies to read with him, recognising she may be opening him up to being called to serve the Lord far away.
Everyone who finds God has done their own seeking. She cannot force him to seek, but she can demonstrate by her own desire to please God, and her joy in Him (rather than her focus on her son) that He is worth finding. Within this, she must come to terms with the unique person that he is, and resist the temptation to try to turn him out like someone other than the whole person God would have him become.
I wonder whether she and her husband could open their home to other young people more than they do - not necessarily from church - but perhaps associated with charitable work which could draw this young man towards a more wholesome group of friends. Also, he needs a constructive hobby with physical activities or music or both, which are not 'chores'.
I wonder how he could afford to smoke and drink anyway? Does he earn his own money for this? Or was he skipping school meals to afford it? Maybe she could save some of the money she was giving him so as to let him choose a special outing (holiday) or reward to himself for changing his ways. If there's something he wants enough, this strategy may work - especially if it takes a while to save enough.
All the while I'm aware that a non-Christian father will bring a mixture of influences to the boy's life. He needs them all, because in the end only he can choose to be different from his dad, and some things he will learn are life skills which he most certainly needs. That his dad is in a stable marriage is a great example. He knows how to hold down an exclusive love relationship with one woman. That's quite a treasure for her son. Maybe he's going to learn how to hunt and build or make money through trade or other survival skills. These must be embraced wholeheartedly as far as possible."