U.S. Border Patrol agents take a father and son from Honduras into custody near the U.S.-Mexico border on June 12, 2018 near Mission, Texas. The asylum seekers were then sent to a U.S. Customs and Border Protection (CBP) processing center for possible separation. U.S. border authorities are executing the Trump administration's zero tolerance policy towards undocumented immigrants. U.S. Attorney General Jeff Sessions also said that domestic and gang violence in immigrants' country of origin would no longer qualify them for political-asylum status. John Moore/Getty Images
PHOTO: John Moore/Getty Images
U.S. Border Patrol agents take a father and son from Honduras into custody near the U.S.-Mexico border on June 12, 2018 near Mission, Texas. The asylum seekers were then sent to a U.S. Customs and Border Protection (CBP) processing center for possible separation. U.S. border authorities are executing the Trump administration's zero tolerance policy towards undocumented immigrants. U.S. Attorney General Jeff Sessions also said that domestic and gang violence in immigrants' country of origin would no longer qualify them for political-asylum status. John Moore/Getty Images
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U.S. Border Patrol agents take a father and son from Honduras into custody near the U.S.-Mexico border on June 12, 2018 near Mission, Texas. The asylum seekers were then sent to a U.S. Customs and Border Protection (CBP) processing center for possible separation. U.S. border authorities are executing the Trump administration's zero tolerance policy towards undocumented immigrants. U.S. Attorney General Jeff Sessions also said that domestic and gang violence in immigrants' country of origin would no longer qualify them for political-asylum status. John Moore/Getty Images
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U.S. Border Patrol agents take a father and son from Honduras into custody near the U.S.-Mexico border on June 12, 2018 near Mission, Texas. The asylum seekers were then sent to a U.S. Customs and Border Protection (CBP) processing center for possible separation. U.S. border authorities are executing the Trump administration's zero tolerance policy towards undocumented immigrants. U.S. Attorney General Jeff Sessions also said that domestic and gang violence in immigrants' country of origin would no longer qualify them for political-asylum status. John Moore/Getty Images
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U.S. Border Patrol agents take a father and son from Honduras into custody near the U.S.-Mexico border on June 12, 2018 near Mission, Texas. The asylum seekers were then sent to a U.S. Customs and Border Protection (CBP) processing center for possible separation. U.S. border authorities are executing the Trump administration's zero tolerance policy towards undocumented immigrants. U.S. Attorney General Jeff Sessions also said that domestic and gang violence in immigrants' country of origin would no longer qualify them for political-asylum status. John Moore/Getty Images
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BROWNSVILLE, TX - JUNE 22: A crying Honduran woman and her child wait along the border bridge after being denied into the Texas city of Brownsville which has become dependent on the daily crossing into and out of Mexico on June 22, 2018 in Brownsville, Texas. Immigration has once again been put in the spotlight as Democrats and Republicans spar over the detention of children and families seeking asylum at the border. Before President Donald Trump signed an executive order Wednesday that halts the practice of separating families who were seeking asylum, over 2,300 immigrant children had been separated from their parents in the zero-tolerance policy for border crossers. (Photo by Spencer Platt/Getty Images)
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(CNN) —  

The Trump administration has more than 2,000 children it separated from their parents in its custody. In a six-day span, that number only went down by six children.

It’s still unknown, though, whether those children were reunited with parents, other family or otherwise transferred out of Health and Human Services custody, and the government has not answered questions about the circumstances of their release.

The stories are heart wrenching.

A Guatemalan woman sued the government after her 7-year-old son was separated from her, and in the middle of those proceedings was able to reunite with her son.

As Beata Mariana de Jesus Mejia-Mejia embraced her son, Darwin, at the Baltimore Washington International Airport for the first time in more than a month, she cried.

“I love you,” she said in Spanish, between sobs.

But thousands more parents remain in limbo.

The Annunciation House, which hosts undocumented immigrants in El Paso, Texas, received 32 separated parents on Sunday upon their release from detention. According to the parents, the average child’s age is 10, and just three of the parents had spoken with their child personally since they were separated.

In an emotional news conference, some of the parents told their stories of trying to find their children in government custody.

One woman, Miriam, from Guatemala, said she didn’t have a chance to say a word to her 4-year-old son before he was taken from her at dawn while he was fast asleep – he was still asleep when they put him on a truck and drove away, she said.

When she was finally able to reach him Monday by phone in New York, she said he refused to speak to her. CNN was unable to confirm how much time had passed since their separation. But as Miriam tells it, it was long enough to make an impression on him.

“He’s mad at me,” she said, tears in her eyes. “He thinks that I abandoned him.”

Data hard to come by

The administration has been reticent to release much data about the results of its prosecution policy that ended up separating more than 2,000 families at the border in about six weeks. But the new figures show how slow the pace has been to put those families back together – even as a federal judge has now ordered the government to do so in 30 days.

The government has said it has reunited 538 children with parents they were separated from – though those were children in Customs and Border Protection custody, likely meaning they were never transferred to HHS.

On Tuesday, the secretary of Health and Human Services said there were 2,047 migrant children in its care as a result of being separated from their parents at the border so the parents could be prosecuted on criminal charges. Six days prior, the government had said there were 2,053 such children.

That day, June 20, was when President Donald Trump signed an executive order reversing course on his administration’s decision to separate families – ordering they be held together even during prosecution. In implementing the order, Border Patrol within hours stopped referring parents for criminal charges, thus effectively ending the “zero-tolerance” policy for the time being.

Late Tuesday night, a federal judge in California issued a nationwide order that required the administration to stop detaining immigrant families separately, aside from special circumstances; to reunify parents with children under the age of 5 within two weeks; and to reunite parents with any children aged 5 and over within 30 days.

Asked to explain where the six children went, whether any new separated children had come into the system in the same timeframe and how the court’s ruling would be implemented, a spokesperson for HHS’ Administration for Children and Families would only provide a blanket statement about reunification being the “ultimate goal.”

“HHS’ Administration for Children and Families is focused on continuing to provide quality services and care to the minors in our Office of Refugee Resettlement-funded facilities and reunifying children and teenagers with a relative or appropriate sponsor as we have done since inheriting the program,” the spokesperson said. “Reunification is always the ultimate goal of those entrusted with the care of unaccompanied alien children, and we are working toward that for those unaccompanied alien children currently in our custody.”

In a conference call with reporters on Tuesday, a spokeswoman for HHS pointedly shut down a reporter asking whether the agency was still getting separated children from DHS, and said the agency would not be answering any data or policy questions on the call – only procedural ones.

The Department of Homeland Security, which is detaining the parents who were separated from their children and runs any family detention shelters used to house parents and children together, did not respond to a request for comment about implementing the order Wednesday morning.

’A startling reality’

In his order Tuesday night, Judge Dana Sabraw had strong words for the government’s handling of the issue.

“This is a startling reality. The government readily keeps track of personal property of detainees in criminal and immigration proceedings,” Sabraw wrote. “Yet, the government has no system in place to keep track of, provide effective communication with, and promptly produce alien children. The unfortunate reality is that under the present system, migrant children are not accounted for with the same efficiency and accuracy as property.”

Once a parent was handed over to federal law enforcement for criminal charges, under the “zero-tolerance” policy, the children were given to HHS and treated under the same procedures as the more than 9,000 other migrant children in HHS care who came to the US by themselves.

But those procedures mean that releasing those children back to their parents has to go through a series of hurdles. They can either be reunited with parents when they’re about to be deported, or if the parent is released from detention and applies to be a sponsor, under HHS rules. Any sponsor – usually a parent, relative or family friend – must go through a fingerprint and background check, a process that usually takes weeks.

CNN’s Catherine Shoichet, Emanuella Grinberg and Dianne Gallagher contributed to this report.

CLARIFICATION: This story has been updated to clarify the fate of the six children is not known.