The old LCMS and current WELS doctrine of fellowship is grounded in Scripture’s teaching that Christians must not worship with anyone who causes divisions contrary to what they have been taught (Romans 16:17). That verse does not forbid an individual Christian from praying with a weak believer who is not causing divisions and who is eager to learn and believe all of Scripture but who is led astray by false teaching. Rather, it refers to those who continue to support false doctrine even after the error is exposed to the light of God’s word.

Professor James Pope, at Martin Luther College, explained:

When Christians are joined together in faith and doctrine, they are able to express their unity by joint prayer and worship, cooperative educational endeavors and shared outreach efforts (Acts 1:14; 2:42; Hebrews 10:24-25; Psalm 78:4-7; 3 John 5-8).

When you and I interact with Christians whose faith differs from ours, we follow Scripture’s instructions and do not engage in those previously mentioned activities (Romans 16:17; Titus 3:10; 2 John 10-11).

By not worshiping or praying together with other Christians, you and I are not intending to say that we do not consider such people to be outside the faith. God alone can see what is in the heart (1 Samuel 16:7). We readily and happily acknowledge that the kingdom of God is bigger than our synod. Refraining from prayer and worship with people who are not united with us in faith and doctrine is, as our Catechism points out from Scripture, a matter of showing love for the truth of God’s word (2 Corinthians 13:8), love for our own souls (Galatians 5:9) and love for those who are mixing error with truth (James 5:19-20).

. . .

Praying with family members involves the same principles and application. Then again, you might be dealing with an exceptional situation in which family members belong to a church outside our fellowship, but they are not supportive of their church’s false teachings. In fact, they recognize the errors of their church and are seeking to point others to the truth of God’s word. In a situation like that, their confession of faith may match your confession of faith, and joint prayer in a private setting would not be a cause of offense to others. Exceptional situations like this are spelled out more fully in a book you might find valuable to read: Church Fellowship: Working Together for the Truth . . .”

We rightly join in prayer with Christians who hear God’s word but do not yet understand some teaching of Scripture. On the other hand, it is wrong for a Christian to pray with those who oppose any Scriptural teaching:

If one spouse is a non-Christian, the Christian partner may pray for and in the presence of the non-Christian husband or wife. Obviously, they cannot pray together. If the other spouse is a member of a heterodox church and ridicules or rejects the beliefs of our member, joint prayer is hardly possible. If the other spouse’s membership in a heterodox church is seen as a matter of weakness in understanding, joint prayer may be possible in the privacy of the home.

(Brug, p. 149, as quoted on Pastor David Jay Webber’s Lutheran Theology Web Site)

The principles of church fellowship set forth in the Scriptures do not change. God’s Word always remains the same; however, the manner in which these principles are applied may vary as different circumstances arise. The principles of church fellowship are not legalistic rules but loving directives of the Lord for the good of his church. They must be applied in the spirit of the gracious Savior who loved us so much that he gave his life for us. There will be times when prayer together with other Lutheran Christians or even with Christians of other denominations may be proper, such as when it is apparent that their membership in the false church body is the result of a weak faith which does not fully understand the error of the church body, or it is clear that they actually do not share in the error at all. In such situations one must consider more than the confession of their church membership. There will be times when it will be necessary to attend the worship services of an erring church, such as at the wedding or funeral of a loved one. Here care must be taken so that such attendance is not understood as agreement with the doctrine of the erring church.

The highly individualistic spirit of the times and the abandonment in practice of formal confessions of faith by many church bodies have resulted in many individuals being put in a state of flux regarding their religious convictions and confessions. They do not necessarily hold to the teaching of the church body to which they belong. They may indeed be open to instruction from the Word and may be seeking direction. When such individuals come to us, we cannot always deal with them solely on the basis of their formal confession of faith which they make by their formal church membership. One has to also consider their informal confession of faith. However, this informal confession too must be considered on the basis of the true marks of the church.

(Schmeling, pp. 46-47, as quoted on Pastor David Jay Webber’s Lutheran Theology Web Site)

The article “Prayer fellowship,” by Pastor Nathaniel Biebert, has helpful illustrations and practical applications alongside the supporting passages of Scripture.

The WELS statement on fellowship makes the same distinction between praying with weak believers but not with those who cause divisions, citing several Scripture passages:

4. Weakness of faith is in itself not a reason for terminating church fellowship, but rather an inducement for practicing it vigorously to help one another in overcoming our individual weaknesses. In precept and example, Scripture abounds with exhortations to pay our full debt of love toward the weak.
a. General exhortations. Gal 6:1-3; Eph 4:1-16; Mt 18:15-17.
b. Weakness in laying hold of God’s promises in a firm trust. Mt 6:25-34.
c. Weakness with reference to adiaphora in enjoying fully the liberty wherewith Christ has made us free. Ro 14; 1 Co 8 and 9. The public confession of any church must [on the basis of Scripture] establish, however, which things are adiaphora, so that it may be evident who are the weak and who are the strong. Ro 14:17-23; 1 Co 6:12; 10:23,24.
d. Weakness in understanding God’s truth, and involvement in error. Ac 1:6; Galatians (Judaizing error); Colossians (Jewish-Gnostic error); 1 Co 15; 1 Th 4:10-12,14; 2 Th 3:6,14,15; Ac 15:5,6,22,25. Note how in all these cases, Paul patiently built up the weak faith of these Christians with the gospel to give them strength to overcome the error that had affected them. Compare Walther’s Theses 2, 3, 4, and 8.

5. Persistent adherence to false doctrine and practice calls for termination of church fellowship.
a. We cannot continue to recognize and treat anyone as a Christian brother who in spite of all brotherly admonition impenitently clings to a sin. His and our own spiritual welfare calls for termination of church fellowship (excommunication). Mt 18:17; 1 Co 5:1-6.
b. We can no longer recognize and treat as Christian brethren those who in spite of patient admonition persistently adhere to an error in doctrine or practice, demand recognition for their error, and make propaganda for it. Gal 1:8,9; 5:9; Mt 7:15-19; 16:6; 2 Ti 2:17-19; 2 Jn 9-11; Ro 16:17,18. If the error does not overthrow the foundation of saving faith, the termination of fellowship is not to be construed as an excommunication. Moreover, an excommunication can only apply to an individual, not to a congregation or larger church group. The “avoid them” of Romans 16:17,18 excludes any contact that would be an acknowledgment and manifestation of church fellowship; it calls for a cessation of every further joint expression of faith. Cf. 1 Co 5:9-11. Compare Walther’s Theses 9 and 10.
c. Those who practice church fellowship with persistent errorists are partakers of their evil deeds. 2 Jn 11.