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I am not in your church or situation so it is difficult for me to offer specific opinions. However, I can state some general principles. God's plan is that sexual intimacy be confined to the state of marriage. Unmarried couples who live together really need to get married or else to practice abstinence. Those are the biblical norms. These norms are quite foreign to our modern culture and we encounter many people who are not in conformity with them.
Although Jesus always upheld God's will, he related to sincere people in mercy and not harshly, taking into account human frailties and circumstances. Jesus noted that when David's men were hungry they ate the holy bread of the priests, something normally wrong. The Samaritan woman who encountered Jesus at the well was living with a man not her husband but Jesus spoke to her about living water. The couple you describe are violating God's plan also. But because they are seeking God, they need encouragement, leading and teaching rather than condemnation.
We are called to teach truth and to show mercy, both in Jesus' name. Knowing how to combine and to balance these two tasks in a given situation is not always easy. We want to cure the patient, not kill him. May God give you wisdom and grace to help this couple move into conformity with God's will and to enjoy all the blessing that his commands are intended to convey.
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