McALLEN, Texas — After criminals killed his uncle and cousin and warned that he was next, José fled Honduras fearing for his life. He crossed Mexico with his 3-year-old son and arrived in mid-May at the Hidalgo Port of Entry on the U.S. border to claim asylum.

But even though he entered the U.S. legally at an official border crossing, where the Trump administration promised asylum-seekers would not be prosecuted or separated from their children, José was detained and had his son taken away, according to advocates who are helping with his case.

“When we went to the restroom, they separated me from my son. I asked them where they were going to take him, and they said they were going to take them to another place,” José, 27, said Tuesday through an interpreter in a phone interview. “I asked again, and they didn’t tell me — just that they were taking him to another location. I didn’t even get to say goodbye.”

José, who asked that only his first name be used out of concern for his family’s safety, is not alone. Other migrants, including at least one other father from Honduras, were separated from their children after seeking asylum at official border crossings — “which is what the administration has been saying that people should do,” said Michelle Lapointe, acting deputy legal director of the Immigrant Justice Project at the Southern Poverty Law Center, which is helping José.

“They weren’t prosecuted,” Lapointe said, “but they still had their kids taken.”

While President Donald Trump ordered an end to family separations last week, and a federal judge on Tuesday night ordered that all separated families be reunited within 30 days, the battle is far from over for the parents of the more than 2,000 children who remain apart.

The reunification process has been even slower and more confusing for asylum-seekers, who in some cases had to choose between pursuing their asylum claim while remaining in federal custody, or dropping the claim and reuniting with their children but then face deportation. The separation and prosecution of some asylum-seekers has endangered the legal and internationally sanctioned right of those who have fled violence to ask for refuge in the U.S., lawyers and immigration advocates say.

A spokesperson for Customs and Border Protection said the agency could not comment on individual cases, but gave four reasons families may be separated, even if they are seeking asylum: the criminal or immigration history of an adult in the family; evidence of abuse indicating the child’s safety is at risk; uncertainty over whether family members are truly related; and insufficient detention space to accommodate the family.

Anguished over a child, hard to focus on asylum

Asylum is a form of relief recognized under international law and written into U.S. law. People may seek asylum in the United States if they have been persecuted in their home countries or fear persecution there based on their race, religion, nationality, or membership in a particular social or political group.

Many of the Central Americans who seek asylum in the U.S. say they’re doing so because of gang violence, police corruption and government crackdowns on political opponents back home. The decision to leave, they say, is not one they take lightly — and being separated from their children upon arriving in the U.S. is not something they expected.

At the Port Isabel detention center in Texas, dozens of mothers and fathers who had hoped to win asylum for their families have been so tormented by not knowing where their children are, said attorneys who visited the parents late Sunday, that it’s been hard for them to focus on pleading their case for safe haven in the U.S.

One father from Guatemala told the attorneys that as he made his case to an asylum officer recently, he grew upset when asked whether he had spoken to his child. The father was in the middle of his “credible-fear” interview, an important stage in the asylum process, in which migrants must convince an asylum officer that they deserve to have their case referred to an immigration court, where they will be allowed to explain their situation to a judge.

“He just broke down,” said Natasha Quiroga, a senior counsel with the nonprofit Lawyers’ Committee for Civil Rights Under Law. “The asylum officer stopped the interview and let [him] call the child.”

These so-called credible-fear interviews — the first step in determining whether migrants are held in detention or assigned to a resettlement agency to find housing and employment while waiting to see an immigration judge — are already difficult for asylum-seekers without the added element of family separations, said Sophia Gregg, a lawyer with the Legal Aid Justice Center in Virginia. The hearing “is all about your asylum claim and the persecution you’ve faced, which is hard enough to talk about,” she said. Migrants often describe torture, rape and witnessing the killing of family members.

But in many cases, the persecution the migrants left home to escape becomes secondary to the fact that their children were taken away, said Eileen Blessinger, a Virginia immigration lawyer who went to Texas to help migrant families.

“I don’t think I could coherently give an interview to someone if I didn’t know where my child is,” she said.

The separations could have long-lasting consequences for the families’ safety and well-being, said César Cuauhtémoc García Hernández, an associate professor at the University of Denver Sturm College of Law who writes about criminal and immigration law.

“The trauma that spurred their migration is only augmented by the trauma that occurred at the moment that the parents were separated from their children and then being sent to a detention center,” he said. People claiming asylum, he added, “have gone through a nightmarish situation where they’re coming from, and the Trump administration’s family separation policy made absolutely no attempt to treat those people in a humane fashion.”

The long road to asylum

Asylum cases are difficult to win — only 20 percent of applications were granted last fiscal year, according to U.S. Citizenship and Immigration Services, which handles some cases.

The cases are getting even harder after Attorney General Jeff Sessions ruled this month that people fleeing domestic or gang violence are largely ineligible for asylum, putting many Central American asylum claims in jeopardy.

Not all of those with legitimate asylum claims arrive through an official port of entry — some migrants may not realize they have a strong case and decide to cross the border illegally instead. Under Trump’s “zero-tolerance” policy, they all faced prosecution, and immigration advocates worry that people with legitimate asylum claims are being prosecuted and deported.

That was a concern raised by Hilarie Bass, president of the American Bar Association, after she spent time in U.S. District Court in McAllen, Texas, on Tuesday, watching as about 70 migrants faced charges of crossing the border illegally, a misdemeanor.

Before the court proceedings, the migrants, with their ankles shackled, each spoke to a federal public defender. Bass said she was concerned that the Trump administration’s policy was taxing the lawyers’ ability to adequately explain to migrants what they are legally entitled to.

“Having two to three minutes with a public defender is a completely inadequate amount of time to explain to these people what their legal rights are that they have and what they are waiving by pleading guilty,” Bass said, based on her observations in court. “In particular, we were told by the public defenders that they didn’t even get to analyze whether any of these people did have a legitimate claim to asylum.”

Marjorie Meyers, federal public defender for the Southern District of Texas, said the district's lawyers are spending time with clients according to the clients' needs and the criminal charges they face.

While the lawyers in the public defender's office do not have time to delve deeply into asylum law with every migrant, they do check the circumstances that drove them to the U.S., she said. The lawyers explain to the migrants that they can choose to go to trial and use the need for asylum as a defense. But many migrants opt to plead guilty to illegal entry because that resolves their cases quickly and still gives them the option of applying for asylum later.

For those who do claim asylum, the process can take months. Some applicants spend that time awaiting a decision in detention, while others are eventually released into a monitored supervision program where they get help finding a job and housing.

Asylum seekers who have been separated from their children can apply to sponsor them once they are released from detention. But those who remain detained have been told that they can’t get their children back until they are released from detention. (It’s unclear how the federal judge’s Tuesday ruling could speed this process.)

José recently passed his credible-fear interview, after describing the violent threats he faced at home. But he is still being held at a detention center in Georgia waiting for a court date in his asylum case, and he has not seen or spoken to his son in more than five weeks (Lapointe said the boy is in government custody in Arizona).

“I miss him very much,” José said. “He is very young, and I have always been with him.”

CORRECTION (June 28, 2018, 12:14 p.m. ET): An earlier version of this article misidentified a lawyer who is advocating on behalf of migrant parents, including José. She is Michelle Lapointe, acting deputy legal director of the Immigrant Justice Project at the Southern Poverty Law Center, not Michelle Brané, director of the Migrant Rights and Justice program at the Women’s Refugee Commission.