After securing the approval of his congregation, Bowman defended himself successfully in court and was able to settle his brother's estate. Somewhat later, evidently, certain members of the congregation became dissatisfied with Bowman's use of the court, which was basically a violation of Brethren principles as set forth by the Annual Meeting. A congregational council was held to consider the charges against Bowman, and as a result he was disfellowshiped.
Bowman believed that the action was unjust and proposed to appeal his case to the highest court of appeal in the church, the Annual Meeting. However, the Civil War now made it impssible for him to attend the meetings which were held in the North after 1861. Consequently, he simply continued his actions as an elder, preaching, baptizing, and holding love feasts. Those Brethren who followed him in his action became known as Bowman Brethren. His followers grew to about 130.
The murder of Bowman in 1863 came before it was possible for him to appeal his case to the Annual Meeting and also left his flock without a shepherd. His concern and that of his followers was presented at the Annual Meeting of 1866. The Annual Meeting accepted the need for an investigation and followed its routine practice of appointing a committee. The investigation was most thorough in its character, and the result was the committee decided that Brother John A. Bowman had been unjustly disfellowshiped because he had only done what the church had granted him permission to do.
The members of his church were to be received back into the full fellowship of the Brethren Church without being rebaptized. This event in the life of the church evidently was one of the rare occasions in which a division ended happily, except for the death of John A. Bowman.
Source: The Brethren Encyclopedia