More than 400 migrant children remain separated from their parents and under the federal government's care, according to court documents filed this week.

In late July — the deadline set by a federal judge for the U.S.to reunite more than 2,500 migrant families separated at the southwest border — federal agents had successfully reunited more than half of affected children with their parents. Now, the number of children that remain separated as a result of the Trump administration's "zero tolerance" policy hovers at 416, dozens fewer than reported in last week's status update.

Amid the ongoing reunification effort for these migrant families was Thursday's news of the Department of Homeland Security's decision to change the longstanding Flores agreement, which requires the government to hold immigrant children in the "least restrictive setting" and generally release them after 20 days in detention.

The department announced that it would instead adopt proposed regulations that would allow the government to detain migrant families for longer periods of time. This is a move that will almost certainly invite more legal pushback from advocates.

In the meantime, here's a closer look at how the government broke down the latest numbers and what could happen next with the family reunification process.

What are the latest numbers?

It's been about two months since U.S. District Court Judge Dana Sabraw ordered the U.S. government to reunite these families. In a status update Thursday, the government said of the 2,654 separated migrant children, 2,181 have been "discharged," meaning they were either reunified with their parents or placed with a sponsor within the U.S., among other circumstances, such as the child turning 18 years old.

As of Sept. 4, 2018, 416 children remain separated from their parents. This is about 80 children fewer than last week's update. Of those 416 children, 14 are under age 5.

The parents of 304 children are located outside the U.S. — either because they were deported or because they sent their children to the U.S. with other family members. Both the U.S. and the American Civil Liberties Union have been focusing efforts on resolving these cases due to the difficulty in reaching the adults in their home countries. Sabraw has requested more transparency and information on this group of families, saying last week that the U.S. ought to avoid the "natural tendency to treat each person as a number."

Here's how the U.S. further categorizes the parents of the 416 children that remain in U.S. custody:

304 have adults who are currently outside the U.S.

199 belong to parents who "indicated desire against reunification." It should be noted that the ACLU has challenged this supposed "desire" in court, filing personal court documents that say some parents may have been coerced by immigration officials to waive their reunification rights.

31 adults had a "red flag" in their background checks

9 adults are in federal, state or local custody

3 adults had a "red flag," concerning safety and well-being

Comparing this breakdown with last week's numbers, two categories have disappeared. The U.S. said a group belonging to one of the previously reported categories — children who were still under U.S. care "where further review shows they were not separated from parents by DHS" — has been determined to no longer be eligible class members in the ongoing lawsuit. The U.S. said it will provide ACLU attorneys with a "line list" of the 57 cases that remain in this group.

Another category, "adult red flag case review — parentage," was also absorbed by the new "out-of-class" category, after a final determination found these cases did not result from separations by DHS officials.

The U.S. said in the status update that it intended by Friday to provide reasoning for any parent who has been removed as a class member from the lawsuit. These may be parents who have not yet been reunified "due to concerns related to criminal history, fitness, or danger," the U.S. said in court documents.

The ACLU is "particularly concerned" about some of the "red flag" cases

ACLU said in the status update that it and its network has made "significant progress" getting in touch with separated parents, and also confirming that they wanted to be reunified with their children.

However, the organization pointed to two "red flag" cases deemed ineligible for reunification that "may require expedited attention."

ACLU said it was "particularly concerned" about a 4-year-old whose mother was denied reunification because of an outstanding foreign warrant that says she's a gang member. The mother has denied the allegation.

At her immigration bond hearing, "the immigration judge expressly found that this warrant was not sufficient evidence that the mother was a danger to the community."

But because of the mother's supposed criminal history, the U.S. has denied her reunification with her child, who was 3 years old when he was first detained, ACLU said.

"This child is suffering greatly in detention and is at particular risk of grievous and irreparable harm," the organization wrote.

In a second case, a father was denied reunification with his 2-year-old son. The U.S. appeared to base its decision on the father's criminal history. The ACLU said it was aware of the adult's guilty plea for assault in 2010, but that the incident "has no bearing on his current dangerousness or ability to care for his child."

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