We are truly sorry to hear about the separation you're experiencing. Firstly, we want to remind you that God's desire is for reconciliation and restoration, but it should be aligned with His will and His ways, and this is always done best in a marriage.
In cases of separation, God's word tells us to strive for peaceful and pure relationships. We read in Hebrews 12:14 WEB, to "Follow after peace with all men, and the sanctification without which no man will see the Lord." Also, 2 Corinthians 6:14 WEB tells us, "Don’t be unequally yoked with unbelievers, for what fellowship have righteousness and iniquity? Or what fellowship has light with darkness?"
God's will is for you both to be believers pursuing purity, peace, and godly lives. So, we pray that if your significant other is not a believer, that they would be drawn to Jesus Christ first.
Regardless, you both should be focusing on a pure and godly relationship. We should be encouraging you to be pursuing a marriage and not just a relationship. This is especially important with a child involved. If you are not married, please let us know so that we can discuss this further.
As for healing and working on your differences, we read in Colossians 3:13 WEB, "bearing with one another, and forgiving each other, if any man has a complaint against any; even as Christ forgave you, so you also do." Also, remember the love that God has for you both, as it says in Romans 8:37-39 WEB, "No, in all these things, we are more than conquerors through him who loved us. For I am persuaded, that neither death, nor life, nor angels, nor principalities, nor things present, nor things to come, nor powers, nor height, nor depth, nor any other created thing, will be able to separate us from the love of God, which is in Christ Jesus our Lord."
Knowing this, we should be praying in the name of Jesus Christ. We should not be just praying to God without Jesus Christ. It is only through Jesus Christ that we can be saved, Acts 4:12 WEB "There is salvation in none other, for neither is there any other name under heaven, that is given among men, by which we must be saved!" It is also only through Jesus Christ that we can pray to God, John 14:6 WEB "Jesus said to him, “I am the way, the truth, and the life. No one comes to the Father except through me."
So, let us pray together.
Dear Heavenly Father,
We come before You in the name of Jesus Christ, lifting up this family that is in need of Your healing touch. We pray that You would work in the hearts and in both of their lives, and draw them both to Jesus Christ first. We pray that You would restore this relationship only if it is Your will and only in a way that would bring glory to Your name. We pray that both would be believers in Jesus Christ if they are not already. We pray for a godly marriage and for a restoration of this family unit.
Help them to bear with each other and forgive each other, just as Christ has forgiven them. Guide them as they strive for a peaceful and pure relationship, and give them the wisdom to work on their differences in a way that honors You.
We ask all of this in the precious name of Jesus Christ, our Lord and Savior. Amen.