Nazario said he and Filomena trekked across Mexico to the U.S. border to seek asylum after his life was threatened by gang members in Guatemala. After being locked up for two weeks, he gave up his asylum claim because he said he was told it was the swiftest way to be reunited with his little girl. Instead, he was flown back to Guatemala without Filomena.

Nazario's case should actually be simpler than that of other deported parents, according to immigration experts. Unlike many detained immigrants, Nazario had help from pro bono attorneys and officials with the Guatemalan consulate who located Filomena in New York, and helped Nazario submit all the documents the government required to bring them back together.

The U.S. Department of Homeland Security, which oversees immigration authorities, did not return KQED's requests for comment on Filomena's case.

'I definitely am afraid that parents who’ve been deported will never see their children again.' Erika Pinheiro, attorney with L.A.-based non-profit Al Otro Lado

But a high-ranking official with U.S. Immigration and Customs Enforcement (ICE) told reporters on a recent call that, although the agency plans to continue its reunification efforts, it may not know the location of every parent whose kids were taken.

"We don't keep track of individuals once they've been deported to foreign countries," said Matthew Albence, who oversees deportations for ICE.

He added: "We will work with the court and look at the process to how we could potentially facilitate reunification of these individuals, should these individuals want reunification."

In a report last week to U.S. District Judge Dana Sabraw in San Diego, lawyers for ICE said parents for 120 children in federal custody "waived reunification." But filings by the ACLU question whether the parents understood the documents they were signing.

Nazario says he has always wanted to be reunited with his daughter.

Erika Pinheiro, an attorney who is helping the family, said the process should be straightforward and she is baffled by the delays. But for separated families who lack legal help, the obstacles could prove insurmountable.

"I definitely am afraid that parents who’ve been deported will never see their children again," said Pinheiro, with the Los Angeles-based non-profit group Al Otro Lado.

Many of the deported parents are from hard-to-reach, rural areas in Guatemala, Honduras and El Salvador. Pinheiro said it may be difficult to find them if they are still fleeing persecution.

"Sometimes they can't stay at home, you know, they're facing immediate danger or death. And so by definition they're going to be on the move to try to find a safe place," she said.

Many child development and health experts say kids like Filomena who languish in government custody without their parents could suffer lasting trauma.

"Forced separation disrupts the parent-child relationship and puts children at increased risk for both physical and mental illness," reads a letter to DHS Secretary Kirstjen Nielsen from leaders with 540 organizations with expertise in child health and welfare.

That's why reuniting these families is urgent, said Michelle Brané, with the Women’s Refugee Commission in New York City. Her group and other U.S. non-profits have reached out to organizations in Central America to locate deported parents and get them legal assistance. But she says those ad hoc efforts should not be a substitute for official action.

"It is the government's responsibility, who separated them wrongly, to reunify them. So they need to find them," she said.

In Guatemala, Nazario said he and his wife Marcela are debating whether to give up the small parcel of mountainous land where he grows potatoes -- to avoid the gang violence. First, though, he must get Filomena back.

"Once I have my daughter, I'll see if we leave or if we stay home," he said.

NOTE: KQED originally spelled Filomena's name Filemona, as it appeared on a U.S. court document filed by her father. In fact, her name is spelled Filomena and appears that way on her Guatemalan birth certificate.