The Schaibles were already on 10 years' probation in the 2009 death of son Kent, 2, who also died of bacterial pneumonia while they prayed and did not seek medical treatment.
Since Brandon's death, the Schaibles' seven remaining children have been in foster care.
Pescatore urged Common Pleas Court Judge Benjamin Lerner not to lift a detainer that would have let Schaible post $250,000 bail raised by the congregation.
Lerner agreed, saying, "Right now, both defendants are in custody, and at least one of them clearly will remain in custody."
Clark could not be reached for comment and Lerner ordered Pescatore and the Schaibles' lawyers not to discuss the letter with reporters.
But the issue is likely to come up again Friday when Catherine Schaible returns to Lerner's courtroom for her own hearing.
Herbert Schaible - tall, gaunt, and dressed in denim shorts and green T-shirt - displayed no reaction to his pastor's letter.
Defense attorney Bobby Hoof said it was the first he had heard of the letter.
"He does deny being a domineering, unbearable force that he is perceived to be" by Clark, Hoof said.
Hoof told Lerner that Schaible's father-in-law, William R. Wakefield, and brothers David and Richard were in court to support him.
Before he was led away to return to prison, Schaible turned and nodded to the three men. None would comment afterward.
Discussing Clark's letter in court, Pescatore gave no indication of why it was written or its significance within the insular church.
The letter could indicate division in the church hierarchy about the case. It could also be an attempt to buttress Catherine Schaible's case to be released and able to visit her children.
Clark attended the Schaibles' first trial in 2010 and spoke on their behalf after they were found guilty of involuntary manslaughter in Kent Schaible's death.
Clark, however, was not the clergyman in the house praying with the Schaibles when their sons died. That was Assistant Pastor Ralph Myers.
On Tuesday, Lerner offered Catherine Schaible's attorney, Mythri Jayaraman, the chance to present more evidence to convince him Schaible can be trusted to follow court orders if released.
Contact Joseph A. Slobodzian at 215-854-2985, firstname.lastname@example.org, or @joeslobo on Twitter.