(CNN) —  

One thing that’s clear from President Donald Trump’s executive order trying to reverse course from his policy that resulted in family separations at the border: It’s still not clear how it will work.

Officials across the government were hurriedly meeting Thursday to try to come up with clear guidance on the implementation. Agencies gave few answers – and sometimes corrected those answers – about what the order meant.

Trump’s move itself seemed to come together hastily Wednesday with reports about the imminent order leaking out even as key lawmakers in Congress and a source inside one of the agencies that would carry out the order saying they did not know what was going to be in it.

The executive order the President signed kept in place the “zero-tolerance” prosecution policy that resulted in families caught crossing illegally at the border being separated because the adults are charged with a crime, but it said that the administration would aim to keep families together during that process going forward.

But that left a number of questions unanswered, not the least of which was what would happen to the more than 2,300 children now in government shelters all over the country who had been separated from their parents since the policy went into effect in April and whether those families would be reunited.

Even more questions remained about how families could be kept together while the adults were also charged with a crime, why they were ever separated in the first place if that was an option, and what would happen to the families after 20 days, when a court settlement requires children to be released from detention.

“Discussions regarding implementation of the executive order are still ongoing,” an administration official said Thursday afternoon.

Meanwhile, conflicting messages emerged from the administration.

Asked about how families will be reunified on Capitol Hill on Thursday, Homeland Security Secretary Kirstjen Nielsen said there was a plan that seemed to refer to the current procedure placing the responsibility on the parents to track their children down in the custody of the Department of Health and Human Services by calling government hotlines.

“We have a plan to do that, as you know we do it on the back end,” Nielsen said. “So a combination of DHS, DOJ, HHS reuniting as quickly as we can. But don’t forget the vast majority of those kids are (unaccompanied), so we have to find them someone.”

Nielsen appeared to be referring to the roughly 80% of children in HHS custody who came to the US illegally alone, but there are more than 2,000 children who were still separated from their families as a direct result of her agency’s decision to refer the adults for prosecution.

Nielsen then ignored a question about what happens when the 20 days are up.

Trump himself muddied the waters on Thursday, saying at a White House event that separations may continue, which appeared to be an attempt to continue to falsely blame Democrats for his own policy even as his executive order reversing course demonstrated that he had the ability to change it even when he had been insisting he didn’t.

“Democrat and court-ordered loopholes prevent family detention and lead to family separation, no matter how you cut it,” Trump said. “I signed a very good executive order yesterday, but that’s only limited. No matter how you cut it, it leads to separation ultimately.”

And a Justice Department filing seemed to say that the executive order’s way to keep families together – by keeping them in DHS custody through their court proceedings – was not possible.

“Under current law and legal rulings, including this Court’s, it is not possible for the U.S. government to detain families together during the pendency of their immigration proceedings. It cannot be done,” federal attorneys wrote to the judge asking to have the 20-day restriction she imposed waived.

Meanwhile, a Customs and Border Protection spokesperson put out a statement to the media that the agency “has taken immediate steps” to put the order into effect, and that families would be kept together and transferred to family detention if they were caught crossing the border illegally.

“The Border Patrol will continue to refer for prosecution adults who cross the border illegally,” the statement said, adding that any children still in Border Patrol custody – likely a small number as Border Patrol has been quickly transferring children to HHS when separated from parents – would be reunified with their parents after any criminal proceedings.

But according to email traffic sent Wednesday night and Thursday morning that was obtained by CNN, Customs and Border Protection has told its field offices to suspend referring any parents who cross the border illegally with their children for prosecution for misdemeanor illegal-entry charges. The move, which could be reversed, effectively neuters “zero tolerance” as long as it is in effect.

In different email traffic obtained by CNN, it was clear there was plenty of confusion in the aftermath of the executive order.

The order requires families to be held together, meaning they will need to be kept in detention space that is designed for families.

But late Wednesday evening, after the executive order was signed, an Immigration and Customs Enforcement official sent a notification that the family detention centers ICE runs would close for three days. Those would be the places families are sent if they are to be detained together, as the order maintains.

The notice said families could not be sent there in the meantime.

By Thursday afternoon, a different ICE official said the residential centers were back open and to spread the word, allowing for families to be transferred again.

The statements and miscues followed further mixed messaging from the administration on Wednesday.

Hours after the order was signed, the White House convened a call for reporters with Gene Hamilton, the counselor to the attorney general, who said he could not answer implementation questions. While Hamilton said the order would have “immediate effect,” he demurred on what exactly it would be, citing that the order acknowledges that implementation will be subject to what resources are available.

“There will be an implementation phase that follows. Certainly (DHS) and (HHS) will be working and collaborating closely on the best way to implement this executive order,” Hamilton said. “I can’t say what they’re going to do. … The President’s executive order makes clear what the policy is going forward.”

And HHS put out a statement only to walk it back without further clarity hours later.

“For the minors currently in the unaccompanied alien children program, the sponsorship process will proceed as usual,” HHS spokesman Kenneth Wolfe told CNN.

Later Wednesday, the agency put out a statement from Brian Marriott, a senior communications official at the Administration for Children and Families, the same division of HHS where Wolfe works. Though the statement said Wolfe “misspoke” about the executive order, Marriott did not say a clear plan for putting children back with the parents they had been separated from was in place.

“It is still very early and we are awaiting further guidance on the matter,” Marriott said. “Our focus is on continuing to provide quality services and care to the minors in HHS/ORR funded facilities and reunifying minors with a relative or appropriate sponsor as we have done since HHS inherited the program. Reunification is always the ultimate goal of those entrusted with the care of UACs, and the administration is working towards that for those UACs currently in HHS custody.”

CNN’s Kevin Liptak contributed to this report.