But on Thursday, a judge was to hear from their attorneys, along with attorneys for their parents and Child Protective Services, on whether the children ought to be returned to the ranch run by a polygamous sect or be placed in permanent foster care.
"Our attorneys are going to take all the evidence we have and make a case for keeping the children in our care," CPS spokeswoman Marissa Gonzales said.
Tom Green County Judge Barbara Walther signed an emergency order nearly two weeks ago giving the state custody of the children after a 16-year-old girl called an abuse hot line claiming her husband, a 50-year-old member of the sect, beat and raped her. The girl has yet to be identified by investigators.
Authorities raided the Eldorado ranch and spent a week collecting documents and disk drives that might provide evidence of underage girls being given to adult men in marriages by the Fundamentalist Church of Jesus Christ of Latter Day Saints, which owns the ranch.
The children, first taken to shelters in Eldorado, were later moved to a historic fort and then to a domed coliseum on the fairgrounds in San Angelo. All but 27 adolescent boys are staying in the coliseum and a nearby building; the teenage boys are at a boys ranch near Amarillo.
If Walther gives CPS permanent custody of the children, the agency will begin looking for foster homes in a case that has already stretched the legal resources of this small town and the state's child welfare system.
The custody case is one of the largest in U.S. history and involves children from six months to 17 years in age. Roughly 100 of the children are under age 4.
Responding to criticism that the raid on the compound has destroyed the lives of the families, Texas Attorney General Greg Abbott told CBS' The Early Show the state's goal is to protect the children and remove them from any alleged "dangerous situation."
State officials contend the children were being physically and sexually abused or were in imminent danger of such abuse. In initial court filings, they said girls were forced into spiritual marriages - relationships ordained by the church but not legally recognized - with adult men and that boys were conditioned to be abusers as they grew up.
FLDS members say the state is persecuting them for their faith and that their 1,700-acre Yearning for Zion Ranch, with its soaring white temple and log cabin-style houses, is simply a home isolated from a hostile and sinful world.
They deny children were abused.
"It's the furthest thing away from what we do here," said Dan, a sect member who spoke at the compound Wednesday but declined to give his last name because he fears how it will affect his children in state custody. "There's nothing that's more disliked and more trained against."
Flora Jessop, a former wife in a polygamous sect who later escaped, defended the state's handling of the situation. "Texas did the right thing," Jessop told The Early Show. "They went in to help the child. Regardless of what happens, the system worked."
Attorneys for the parents were seen entering the compound Wednesday, and a parade of attorneys recruited by the state bar association was interviewing children at the shelter in advance of Thursday's hearing.
Typically, each child would be given a separate hearing, but given the number of cases, it's likely the judge will have the state, the children's attorneys and the parents' attorneys make consolidated presentations, at least initially, said Harper Estes, president-elect of the state bar.
"You can't go one-by-one," Estes said.
In preparation for the jammed courtroom, the city has installed closed circuit feeds at a nearby auditorium in city hall and a coliseum near where
the children are housed, reports CBS News correspondent Hari Sreenivasan.
If the judge gives the state permanent custody, CPS will have an enormous challenge in finding homes for the children in an already tight foster system.
CPS has relied on volunteers to help feed the children, launder linens and provide crafts and games for them in a dorm-style setting for the past two weeks. But the agency will have to find stable homes and try to decipher sibling relationships that should be preserved if it gets permanent custody.
Even identifying groups of siblings has been challenging so far.
"There's quite a lot of difficulty in identifying how many of these children are biologically related to one another. There's a large number who are half-siblings," Gonzales said.
The children, who dress in pioneer-style clothes meant to emphasize modesty, have been raised in the insular FLDS community.
The sect came to West Texas in 2003, relocating some members from the church's traditional home along the Utah-Arizona state line. It traces its religious roots to the early theology of the mainstream Church of Jesus Christ of Latter-day Saints, which now denounces polygamy and excommunicates members found practicing it.