Synechdoche is a figure of speech that occurs often in literature, including the Holy Bible. It is the convention of mentioning a part when the whole is in view, and visa versa. This explains how a part (such as the human spirit) can sometimes be used to include the soul, and sometimes body for soul. For example: “And it shall be that every soul who will not hear that Prophet shall be utterly destroyed from among the people” (Acts 3:23). That punishment obviously would include the material aspect of man, not just his soul. Thus, some interchangeable use of terms does not disprove that the human soul and spirit are ontologically distinct.
Consider how the persons of the Trinity are sometimes referred to by the names of the Others.
God is triune; He is three persons, yet one God.
“Yet for us there is one God, the Father, of whom are all things, and we for Him; and one Lord Jesus Christ, through whom are all things, and through whom we live.” “One God and Father of all, who is above all, and through all, and in you all.” “For there is one God and one Mediator between God and men, the Man Christ Jesus” (1 Cor. 8:6; Eph. 4:6; 1 Tim. 2:5).
The Holy Spirit is referred to as the Spirit of His Son. “And because you are sons, God has sent forth the Spirit of His Son into your hearts…” (Gal. 4:6).
The Holy Spirit is referred to as the Spirit of Christ. “Searching what, or what manner of time, the Spirit of Christ who was in them was indicating when He testified beforehand the sufferings of Christ and the glories that would follow” (1 Pet. 1:11).
The Son of God, Christ, is distinct person from the Holy Spirit (Matt. 3:16,17). But note how, since God is tri-une, the “Spirit” is used interchangeably with “the Spirit of His Son” as in the next verse in 1 Peter: “To them it was revealed that, not to themselves, but to us they were ministering the things which now have been reported to you through those who have preached the gospel to you by the Holy Spirit sent from heaven–things which angels desire to look into” (1 Pet. 1:12).
Isaiah uses the title “Everlasting Father” of Christ. “For unto us a Child is born, Unto us a Son is given; And the government will be upon His shoulder. And His name will be called Wonderful, Counselor, Mighty God, Everlasting Father, Prince of Peace” (Isaiah 9:6).
Jesus identifies Himself closely with the Father. “Jesus said to him, ‘Have I been with you so long, and yet you have not known Me, Philip? He who has seen Me has seen the Father; so how can you say, ‘Show us the Father’?” (John 14:9).
Yet, God the Son and God the Father are distinct persons in the Godhead: “Then Jesus answered and said to them, ‘Most assuredly, I say to you, the Son can do nothing of Himself, but what He sees the Father do; for whatever He does, the Son also does in like manner. For the Father loves the Son, and shows Him all things that He Himself does; and He will show Him greater works than these, that you may marvel. For as the Father raises the dead and gives life to them, even so the Son gives life to whom He will. For the Father judges no one, but has committed all judgment to the Son, that all should honor the Son just as they honor the Father. He who does not honor the Son does not honor the Father who sent Him” (John 5:19-23).
However, note how the Son and the Father are spiritually united: “At that day you will know that I am in My Father, and you in Me, and I in you” (John 14:20). “I and My Father are one” (John 10:30).
The Holy Spirit is God (Acts 5:4) yet is distinct from the Father who is also recognized as God (1 Cor. 1:3). “And I will pray the Father, and He will give you another Helper, that He may abide with you forever…But the Helper, the Holy Spirit, whom the Father will send in My name, He will teach you all things, and bring to your remembrance all things that I said to you” (John 14:16,26).
Therefore, if terms can be used interchangeable of God the Father, Son, and Spirit without contradicting the doctrine of God’s tri-unity, even so some interchangeable usage of soul and spirit need not contradict the tri-unity of man (1 Thess. 5:23).