The Saving of the Soul
Spirit v. Soul
When a man comes to Christ and is born again, it is his spirit man which is recreated, not his body or his soul. His body remains as it was, tainted with corruption to be glorified into incorruption when the Lord returns. His soul may receive flashes and impulses from his newly made alive spirit, but it remains mostly as it was. He has to develop his soul throughout his walk of salvation, meaning he has to learn to exercise his faculties to follow the perceptions and leanings of the spirit man over those of the outer man.
You must understand this, my beloved: let everyone be quick to listen, slow to speak, slow to anger; for your anger does not produce God's righteousness. Therefore rid yourselves of all sordidness and rank growth of wickedness, and welcome with meekness the implanted word that has the power to save your souls. (James 1:19–21)
Here James is dealing with Christians who are quick to anger and engaged in conduct unbecoming their walk. They've been born again, but they haven't yet grown in their souls. "Welcome the implanted word," James says. By “word” he means receiving the word of Christ, his death, burial, and resurrection, and giving it space in their thought life. Implanted, it will save them from engaging in the corruptible acts of the outer man so they can perform acts of righteousness, which are consistent with the new life of their inner man.
Do not be conformed to this world, but be transformed by the renewing of your minds, so that you may discern what is the will of God—what is good and acceptable and perfect. (Romans 12:2)
The development of the soul, in this passage Paul coins it as the “renewing of the mind,” isn't something that God initiates or performs. It's the responsibility of the believer. (We see this in James: “[You] receive the implanted word”). Paul tells the believers in Rome that they must renew their minds so that they can discern God's will. To put it another way, if they don’t bother to renew their minds to the Word and the revelation of the Spirit, they won’t be able to discern God’s will, even his permissible will.
For though by this time you ought to be teachers, you need someone to teach you again the basic elements of the oracles of God. You need milk, not solid food; for everyone who lives on milk, still being an infant, is unskilled in the word of righteousness. But solid food is for the mature, for those whose faculties have been trained by practice to distinguish good and evil. (Hebrews 5:12–14)
This passage in Hebrews marks the distinction between those who have gone on to develop their souls and those who haven't. The author says that those who have trained their faculties to distinguish good and evil, natural or supernatural, may move on to solid food or maturity in Christ. But those who haven’t undertaken the task to develop themselves remain infants, left to suckle on only the rudimentary principles of the faith.