Washington CNN  — 

What strikes Lauren Kostes is the silence.

“It’s just depressed silence. It’s a heartbreaking kind of silence,” she said.

It’s the moment when she tells an immigrant parent they are set to be deported and must choose whether to take their child with them.

“They know that with this, their relationship with their child will be forever changed. And you can clearly see them going through every consequence in their head,” said Kostes, an immigration attorney with legal assistance foundation Florence Project.

Thursday marks a court-ordered deadline for the government to reunite families it separated at the border. Of the nearly 2,600 children the government identified as separated from their parents, more than 460 have parents who are likely to already have been deported without them, something the government says was done with the parents’ consent.

Of the ones still in the US, 900 are facing final orders of removal that could result in them being deported as soon as the federal judge in the reunions lawsuit lifts a temporary hold he put on deporting separated families.

Even before the Trump administration deployed a policy that separated those thousands of immigrant families at the US border, immigration attorneys have at times had to inform clients that their children may have stronger claims to stay in the US than they do as a family. For some families, leaving the child behind is the only way they see to save that child’s life.

Under normal circumstances, that’s a difficult decision. So the American Civil Liberties Union is asking the judge to give parents seven days after reunification to make the decision, given the added trauma and confusion caused by the separation in the first place, as a part of the lawsuit it brought over the separations.

Audio obtained exclusively by CNN of mothers appearing in immigration court while separated from their children gives voice to the anguish they face. “I cannot continue with this anymore. What I want is to be with my son,” one woman pleads with the judge as he tries to conduct a hearing on whether she can pursue asylum in the US.

Those mothers were ordered deported by the judge but remain in the country, CNN confirmed. They have since been reunited with their children.

But for the parents facing deportation, in that moment, they are “thinking, ‘What does this mean? What does this mean for me, what does this mean for my child, what is the best decision?’ ” Kostes said. “It’s a silence of processing and working through every possibility.”

Separations lead to complicated court cases

When the administration began separating migrant families who had crossed the border without permission as part of its “zero tolerance” prosecution initiative, it split their immigration cases as well. Parents remained in detention near the border for the most part, moving rapidly through court dockets historically unfriendly to immigrants’ claims that found hundreds of them eligible for deportation. That process was only compounded by a reinterpretation of asylum law by Attorney General Jeff Sessions that made it nearly impossible for victims of gang and domestic violence to qualify for asylum in the US. Experts say that reversal has especially affected the Central American migrants who try to cross the southern border, thousands of whom cross each month.

The separated children were put into Health and Human Services custody and given their own court proceedings. Court settlements and anti-human-trafficking laws in the US also give children a different set of protections than families and adults have in the immigration system, generally meaning their court cases proceed much more slowly than their parents’ and giving them a better chance of qualifying for protections in the US.

Once the parent is given an order of deportation, they are presented with a form by the government, offering them to either be deported with their child or without.

The separation process is difficult for lawyers as well.

The ACLU has also argued that the separation has made offering legal advice to those families more complicated. Asylum claims require detailed evidence and testimony, and in some cases, the parent or child may have access to evidence the other does not. Parents are under extreme emotional distress during the separation, their attorneys say. Children, meanwhile, are given caseworkers, who may have worked with the child to determine possible claims they have in the US.

When they are reunited, there are other barriers to giving adequate legal advice. In a Wednesday court filing, the ACLU included an affidavit from Manoj Govindaiah of the nonprofit Refugee and Immigrant Center for Education and Legal Services. He described reunited families being inseparable and deeply suspicious of anyone, even those purporting to help.

“In one case, we had been discussing the complicated procedural posture of the father’s and his son’s cases, that he had received a negative expedited removal order and was facing deportation, while his son could still apply for asylum. When he asked for clarification of what that meant, I explained that it could result in his son remaining in the United States without him. We could not complete our meeting because his crying prevented us from effectively discussing his legal case,” Govindaiah wrote.

Kostes said she and her colleagues will often have to counsel the parents over multiple visits regarding their options. The weight of the decision is often too much for one meeting, she said.

With separated parents in particular, she said, many have been asked to make this decision before they have seen their child and with little communication – at best.

“What we are seeing is the parents accept that for the child it’s best for them to stay here, but we’re hearing things like, ‘If they deport me, I just want to say goodbye to my child. I’ll accept deportation but I just want a chance to say goodbye,’ and that’s just really heartbreaking,” Kostes said.

A harrowing choice

Many thus far have opted to be deported alone.

Trump administration officials have portrayed the decision as an easy one. Asked by reporters about the potentially hundreds of parents deported without their children over the course of the zero tolerance policy, officials reiterated the parents had consented.

“Those individuals, as has always been our policy, were provided the opportunity to take their child with them pursuant to their removal. Those individuals declined to do so,” said Matthew Albence, chief of Enforcement and Removal Operations at Immigration and Customs Enforcement. “They are not going to generally take that child back with them after they’ve accomplished their smuggling.”

“Why we’ve seen many of these parents who have been removed decline to take their child is because they completed the smuggling act,” he said in a different call. “That was the intended goal of their illegal entry in the first place.”

The parents for the most part have been charged only with misdemeanor illegal entry to the US, if anything, and not with smuggling.

Attorneys like Kostes, who works with the nonprofit immigrant assistance program the Florence Project, say the reality for these parents is much starker and more difficult.

For many Central Americans, the journey north is spurred by gang threats, according to experts and immigration advocates. In one example, Lenni Benson, a New York Law School professor who’s executive director of the legal assistance program Safe Passage Project, had a recent client on the border who was facing deportation and had to decide whether to take her 17-year-old daughter with her. CNN has agreed to withhold her identity for safety considerations.

The Central American migrant ran a small business back home with her daughter. As the business grew, the blocked-number calls started.

The gangs began to threaten and try to extort her. She changed her number. They found her again and kept calling. Then the gangs began telling the mom, a survivor of assault herself, what her daughter looked like and what time the girl would leave home in the morning.

The mother told Benson the gangs “said that ‘she would pay the price. And I know what they do to people,’ ” Benson recounted the woman telling her.

The mother did not tell her daughter about the threats, but they packed up and sneaked into the US. The two were held together in family detention, but Benson had to tell the mother that if she failed to convince the government to re-hear her plea for asylum, her daughter may have an independent claim because of the nature of the threats.

“It was horrible to say, as a lawyer, as a law professor, as a mother, as a human being,” Benson said. “I said to myself, ‘What would I do?’ I would do what parents have always done and said, ‘My child comes first.’ “

Most of the children whose parents opt to leave them in the US are older, usually 11 and up, Kostes said. They are also likely to have family in the US who can care for them.

CNN spoke with one woman, Jennifer, who was in detention awaiting reunification with her 6-year-old daughter. She has not yet been ordered deported, but said that if she had to make the choice, she would take her child. CNN agreed to identify her only by her first name.

“It was a really hard decision to make. I was going to decide to take my child because I didn’t know what else to do,” Jennifer said of her decision to flee to the US, as translated by CNN. “Of course I would take her (if deported). I can’t leave her. … Thank God I didn’t have to make the decision.”

But Jennifer says she cannot go home to Honduras, where the gangs are threatening her family even after she tried to move to the mountains away from them. “The gangs are everywhere,” she added.

“For those who were going to leave their kids behind … they would do it for a better future for the child,” Jennifer said. “In Honduras, for real, there’s nothing there for them.”

CORRECTION: This story has been updated to reflect that Lenni Benson is a professor at New York Law School.

CNN’s Nick Valencia and Catherine Shoichet contributed to this report.