Hundreds of children who were taken from their parents by U.S. immigration agents this spring won’t be reunited by a court-ordered Thursday deadline because the government believes they are ineligible for reunification. Hundreds more of the recently reunified families may be sent to a Texas detention facility to await quick deportation, a process that advocates fear will force families who have been traumatized by separation to confront whether to leave their children in this country when they are deported.

Government lawyers told U.S. District Judge Dana Sabraw, of San Diego, that 1,012 of the 1,637 parents deemed eligible already had been reunited with their children, and the rest had been approved for reunification and were awaiting transportation. Almost all should be reunified with their children by Sabraw’s Thursday deadline, the lawyers said. But another 914 parents have been determined to be ineligible—either because paternity could not be proven or the parent may have been deemed a danger to the child—including more than half of whom appear to no longer be in the country. Government lawyers said that number could go down, but it appears likely that most were either deported or left the country voluntarily—without their children—before Sabraw’s order on June 26 that separated families be reunited. Those numbers are for parents of children ages five to seventeen. About 100 younger children were covered by Sabraw’s order and just over half of them were reunited by a July 10 deadline.

The San Diego federal judge who ordered that children be returned to their families praised the Trump administration’s efforts on Tuesday to reunify about 1,600 of the 2,500 families separated earlier this year. But during a court hearing, he also expressed concern that hundreds of parents may have been deported without their children. “This is a remarkable achievement,” Sabraw said of the reunification efforts at the end of an hour-long status hearing. But he also criticized the administration for its family separation policy—since discontinued by executive order—and the harm it has done. “Some of this information is unpleasant. It’s the reality of the case. It’s the reality of a policy that was in place that resulted in large numbers of families being separated without forethought as to reunification and keeping track of people. That’s the fallout that we’re seeing. … It appears there’s a large number of parents who are unaccounted for or may have been removed without their child.”

An estimated 900 of the 1,637 parents deemed eligible for reunification have final deportation orders, the government lawyers told Sabraw. They cautioned that not all the orders are “executable,” but it was clear at the hearing that large numbers of newly reunited families face quick deportation or other removal action. The American Civil Liberties Union, which brought the lawsuit that led to Sabraw’s reunification order, has asked for a temporary restraining order barring any deportation for at least seven days after reunification so parents can decide whether to take their children with them or leave them in the United States, where the children could press their own asylum cases. The government opposes that motion, and Sabraw said he’d consider the request at a hearing on Friday. He has issued a stay blocking deportations of reunited families until he rules on the temporary restraining order request.

Government lawyers told Sabraw on Tuesday that they couldn’t immediately say how many of the reunited families are being detained together in government facilities, and how many had been allowed to go free while their immigration cases work through the courts. In a court filing earlier Tuesday, the government lawyers said they had “offered to use the Karnes Family Residential Center exclusively for the reunification of class members subject to final removal orders.” The privately run Karnes facility has been the subject of numerous complaints by people who have been detained there, including allegations of sexual assault or sexual harassment by employees against women in the presence of their children. ACLU attorney Lee Gelernt said the government plans to place about 700 families in the Karnes facility in South Texas, one of the few Immigration and Customs Enforcement detention centers that can handle families, but only 20 or 30 families were there now. Government lawyers didn’t challenge his estimates.