My basic contention, which I have shared with many over the years, is that the salvation and sanctification of our spirit is instantaneous at conversion. We receive Jesus life in our spirit (2 Cor. 5:17). For our body it will also be instantaneous, either when we are resurrected or transformed if we are alive on the earth at Jesus return (1 Thess. 4:13-17). However the salvation and sanctification of our souls however is a process (Jas. 1:18-21). I will come back to this later.
To understand the distinction between spirit and soul it is helpful to lay a scriptural foundation. The scriptures below teach that there is a distinction.
23 Now may the God of peace Himself sanctify you completely; and may your whole spirit, soul, and body be preserved blameless at the coming of our Lord Jesus Christ. 1 Thessalonians 5:23 (NKJV) 12 For the word of God is living and powerful, and sharper than any two-edged sword, piercing even to the division of soul and spirit, and of joints and marrow, and is a discerner of the thoughts and intents of the heart. Hebrews 4:12 (NKJV)
1 Thessalonians tells us there is a distinction between our spirit and soul and Hebrews tells us that while it is difficult, we can understand the distinction by applying His word. The verse below tells us we only need two or three witnesses to establish the truth of something, in this case the truth that spirit and soul are not the same thing has two witnesses above.
1 This will be the third time I am coming to you. “By the mouth of two or three witnesses every word shall be established.” 2 Corinthians 13:1 (NKJV)
While the two witnesses above are sufficient, according to scripture, when we actually apply Heb. 4:12 in practice the spirit and soul distinction become clearer. My qualifier is that I use a bible that is more literal in translation because much is lost in the translations that use more of a dynamic equivalence or paraphrase. This is clearer in the verses below.
9 With my soul I have desired You in the night, Yes, by my spirit within me I will seek You early; For when Your judgments are in the earth, The inhabitants of the world will learn righteousness. Isaiah 26:9 (NKJV) 46 And Mary said: “My soul magnifies the Lord, 47 And my spirit has rejoiced in God my Savior.” Luke 1:46-47 (NKJV)
The tense in the NKJV and the other more literal translations is important. For example the same two verses in the NIV do not clearly bring out the different functions of the soul and spirit.
9 My soul yearns for you in the night; in the morning my spirit longs for you. When your judgments come upon the earth, the people of the world learn righteousness. Isaiah 26:9 (NIV) 46 And Mary said: “My soul glorifies the Lord 47 and my spirit rejoices in God my Savior,” Luke 1:46-47 (NIV)
The important distinction lies in the tenses, particularly in the Luke passage. Something is released by our soul after it has already happened in our spirit. Isaiah speaks of his soul desiring something but using his spirit to encounter Yahweh. Mary tells us that her soul magnifies Yahweh because, past tense, her spirit has already rejoiced in an encounter with Him.
I believe that our soul has three aspects, it expresses our mind, will and emotions. Similarly I believe our spirit has three functions, conscience, communion and intuition. The verses above speak of the result of Isaiah and Mary experiencing or desiring communion in their spirits.
So, back to repentance and sanctification. The task of seeing Christ formed in us is accomplished by submitting the desires of our soul to the leading of our spirit, the place where Christ dwells within ever true believer. Peter, a man who had more than a little experience with this said it well.
22 Since you have purified your souls in obeying the truth through the Spirit in sincere love of the brethren, love one another fervently with a pure heart, 1 Peter 1:22 (NKJV)
Our souls are sanctified when we repent of whatever He reveals to us in our spirits. What we carry from time into eternity is the degree to which the nature of Jesus has been formed in our souls (Gal. 4:19). The question is how our formation is going?