But an examination Thursday in Texas confirmed that Tania’s youngest daughter, called Sofi, suffered from a “serious” heart condition that prompted a doctor to tell Border Patrol agents the girl should remain in the United States. In response, an agent reportedly gave the family a choice: one parent could stay in the country with the children, but the other would have to return to Mexico.

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As the family braced for separation, an agent instructed Sofi to choose between her parents, the mother told NPR, which chose not to report the family’s last name because of active asylum proceedings.

“The agent asked her who she wanted to go with, mom or dad,” Tania told NPR through an interpreter. “And the girl, because she is more attached to me, she said mom. But when they started to take [my husband] away, the girl started to cry. The officer said, ‘You said [you want to go] with mom.’”

Speaking with NPR previously, Tania explained her family was forced to flee Honduras after several horrifically violent encounters. The woman’s mother was reportedly shot nine times, and Tania’s sister-in-law — who witnessed the slaying and was poised to testify in court — was killed afterward, along with her infant daughter.

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Tania knew it was time to escape when a note on her door indicated she had 45 minutes to leave the house, she told NPR. It was reportedly signed by Mara Salvatrucha — also known as MS-13. The family migrated to the United States in April to live with relatives as they waited for asylum, but were sent to Júarez in compliance with Migrant Protection Protocols, also known as the “Remain in Mexico” program.

The family’s story is further complicated by the precarious health of their 3-year-old daughter. Their attorney, Linda Rivas of the nonprofit Las Americas Immigrant Advocacy Center in El Paso, noted in immigration court Wednesday that Sofi was born with a heart condition that required surgery, leaving her with a scar on her chest. Sofi’s medical records showed she had also suffered a heart attack, NPR reported. The parents sought superior medical care for their young daughter in the U.S.

Rivas sought to have the family removed from Migrant Protection Protocols, citing guidelines that state people with “known physical/mental health issues,” should not be subjected to the program. She did not return a request for comment from The Washington Post.

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The judge said he did not have the authority to remove the family from the program, but requested a DHS lawyer to “take note of Rivas’ concerns,” NRP reported. Citing the girl’s health issues the following day, a doctor under contract with the Department of Homeland Security intervened and told an agent the family should remain together in the United States.

The agent reportedly capitulated to the request — on the condition the parents be separated. Only one could stay with the young children in the U.S.

“ . . . I said, ‘I came with the children’s father,’ and [the agent] said, ‘Not him. Only you and your children,'" Tania told NPR. “And the doctor said it’s important for the family to stay [together], and even the doctor said ‘They entered as a family and they have to leave as a family.’”

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Sofi picked her mother, but NPR reported the children latched on to their father as he was taken to another cell. The doctor reportedly returned and persuaded another agent to keep the family together, according to NPR. They were released Friday to a migrant shelter in El Paso, and on Sunday, flew to the Midwest to stay with relatives as they continue to seek asylum.

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The Department of Homeland Security did not provide answers to questions posed by NPR about the family’s treatment. (After this story published, U.S. Customs and Border Protection sent a statement saying the NPR report was false and the girl was never asked to select a parent to stay with her.)

As The Washington Post reported last month, separating children from their parents can cause devastating, lasting effects. Research on child-parent separation has prompted health experts, including pediatricians and psychologists, to oppose the Trump Administration’s border-crossing policy.

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Their heart rate goes up. Their body releases a flood of stress hormones such as cortisol and adrenaline. Those stress hormones can start killing off dendrites — the little branches in brain cells that transmit mes­sages. In time, the stress can start killing off neurons and — especially in young children — wreaking dramatic and long-term damage, both psychologically and to the physical structure of the brain. “The effect is catastrophic,” Charles Nelson, a pediatrics professor at Harvard Medical School, told The Washington Post. “There’s so much research on this that if people paid attention at all to the science, they would never do this.” William Wan, Washington Post

Facing backlash in June for separating migrant families, Homeland Security Secretary Kirstjen Nielsen told a crowd of law enforcement officers “We will not apologize for the job we do.”

NPR’s report comes as the Trump administration attempts to stymie a spate of Central American migrants seeking refuge by crossing from Mexico into the United States, which Attorney General William P. Barr said “completely overwhelmed” the immigration court system.

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The MPP program has proven to be critically important for the Trump administration, as it allows some reprieve for the record number of migrant families crossing into the United States. But Mexico’s Foreign Minister, Marcelo Ebrard, decried the Migrant Protections Protocols program this week and said it was imposed on the country with no recourse.

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A three-judge panel allowed MPP to continue in May, though two of them indicated they had concerns. One judge said it seemed “irrational” to send migrants to Mexico without asking them whether they feared being there. Another said the government is “clearly and flagrantly wrong,” The Post reported.

Rep. Veronica Escobar (D-Tex), told NPR her office helped Tania and Joseph in their quest to be removed from MPP. The congresswoman further requested DHS investigate the allegations raised by the family.

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“It’s an outrage, and it’s absolutely horrifying that a toddler would be asked to choose between two parents. It was just stunning to me,” Escobar told NPR. “It’s one thing to read about it; it’s another thing to actually hear a parent recounting the story firsthand in their own voice.”

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Nick Miroff and Maria Sacchetti contributed to this report.

This story has been updated to include a statement from Customs and Border Protection.