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A divided federal appeals court on Wednesday ordered the dismissal of the case against former Trump national security adviser Michael Flynn, likely concluding a long-running court fight that had taken on greater meaning in political debates about the Russia investigation into the 2016 Trump campaign and about the checks and balances the judiciary has on the executive branch.

Despite Flynn twice pleading guilty for lying to the FBI about his conversations with then-Russian Ambassador Sergey Kislyak during the presidential transition, the Justice Department moved last month to dismiss the case against him. Trial judge Emmet Sullivan of the DC District did not immediately act, instead saying he wanted to weigh the department’s arguments into at least July.

If unchallenged with further appeals, the appeals court’s ruling exonerates Flynn after he sought to change his plea and claimed innocence.

Flynn’s case has become a touchstone for President Donald Trump and his supporters in their criticism of the FBI’s Russia investigation and special counsel Robert Mueller’s criminal prosecution of several Trump campaign associates. Even after the appeals decision, Trump and his supporters continued to attack the investigation, especially as it relates to Flynn. Flynn’s team made public a handwritten note on Wednesday that highlighted then-Vice President Joe Biden’s comments on Flynn in early January 2017 – seeking to again delegitimize the Obama administration’s discussions of the investigation.

Trump weighed in on the ruling on Twitter Wednesday, calling it “Great!” Later in the day, speaking in the Oval Office ahead of a meeting with his Polish counterpart, Trump brought up Flynn unprompted, claiming that his former national security adviser had been “exonerated” and adding, “I want to congratulate him.” And Ohio Rep. Jim Jordan, the ranking Republican on the Judiciary Committee, also touted the court’s decision at a hearing into Attorney General William Barr’s decision-making that began afternoon Wednesday.

A split three-judge panel on the DC Circuit Court of Appeals on Wednesday decided Sullivan didn’t have enough reason to question the DOJ’s prosecution decisions in this case. They also said Sullivan having a third-party attorney weigh in on Flynn’s case, the former judge John Gleeson, isn’t needed anymore.

Sullivan “fails to justify the district court’s unprecedented intrusions on individual liberty and the Executive’s charging authority,” DC appeals court Judge Neomi Rao, a Trump appointee, wrote in the majority opinion.

RELATED: Michael Flynn case is the latest test of separation of powers during Trump years

Appeals court Judge Robert Wilkins disagreed with the decision of Rao and Judge Karen Henderson to short circuit the Flynn case in the trial court immediately. Wilkins wrote he supported allowing Sullivan to hold a hearing about Flynn’s dismissal request on July 16.

Gleeson later asked the trial court for guidance on what happens next, suggesting the case may stay alive for a few weeks.

An attorney representing Sullivan in the appeal declined to comment.

It’s possible the case could continue on in future appeals, given how it is largely about the power of the judiciary, a weighty subject in a case other appeals court judges may take interest in. If Flynn’s case were to stay alive following the ruling Wednesday, it conceivably might not be resolved until after the presidential election, or even next year, if it becomes an issue before the Supreme Court.

Steve Vladeck, CNN legal analyst and professor at the University of Texas School of Law, said on Wednesday the ruling may be “short-lived.”

“Whether or not Judge Sullivan wishes to pursue this further, any of the 11 active judges on the DC Circuit, including Judge Wilkins – who dissented from today’s ruling – can ask the full court to rehear the matter,” Vladeck said. “It is virtually unprecedented for an appeals court to step in at this juncture and order a district judge to rule a particular way on a motion he hasn’t yet ruled on.”

All three judges on the appeals court refused to reassign Flynn’s case to a different judge, as Flynn had hoped. Sullivan has raised questions about whether Flynn should be held in contempt of court for perjury.

The DOJ’s handling of the dismissal in May – including it being filed by an acting political appointee without the endorsement of career prosecutors on the case – also prompted hundreds of former national security professionals and federal prosecutors to criticize Barr for making what they argued were political rather than legally sound decisions on cases involving the President’s friends.

Rao wrote on Wednesday that even the unusual signatures on the dismissal didn’t give the courts enough reason to second guess Barr.

“Each of our three coequal branches should be encouraged to self-correct when it errs. If evidence comes to light calling into question the integrity or purpose of an underlying criminal investigation, the Executive Branch must have the authority to decide that further prosecution is not in the interest of justice,” Rao wrote.

Flynn team attempts to tie Biden to his prosecution

Shortly after the ruling in his favor, Flynn’s legal team made public a new document in his case file that may contribute to ongoing political discussions about the early Russia investigation.

The filing is a handwritten note that would now have little effect in his court case, but can be touted by conservatives that have sought to tie Biden to the 2017 decision to investigate Flynn. The Trump campaign has already seized on the document to attack the former vice president, who has been rising in the polls since becoming the presumptive Democratic nominee.

The Justice Department had sent the note directly to Flynn’s team on Tuesday as part of a review of his case and while keeping it under a court’s protective order. That allowed Flynn’s team to make it public on Wednesday by adding it to his case file as a “supplement.”

While releasing the document, Flynn’s lawyers also suggested that President Barack Obama, Biden, then-FBI Director James Comey and other Obama-era officials plotted against Flynn. These accusation appear to be an attempt to reinforce the “Obamagate” conspiracy theory that Trump has championed about anti-Trump sabotage by Obama officials. There is essentially no evidence of wrongdoing by these former officials, and in a sweeping ruling last year, a judge in the case soundly rejected the allegations that there was a “deep state” plot by Obama-era officials to target Flynn.

The note appears to show an early January meeting where Biden, Obama, Comey and others discussed Russian meddling in the recent election and Flynn. The meeting has been known about for years, and multiple participants testified to Congress that nothing untoward happened regarding Flynn, but that they discussed his controversial and alarming calls with a Russian official.

Flynn’s team called it “stunning and exculpatory,” though it appears that they are leaning into their interpretation of the scattered, handwritten page of notes, which doesn’t prove any wrongdoing on its own.

Flynn’s lawyers say the notes from then-FBI agent Peter Strzok showed that the Obama administration’s leadership discussed whether Flynn’s transition-time call with Kislyak was legitimate. The handwritten note attributes the phrase “Logan Act” to the “VP,” or Biden. But it’s not at all clear what the context of that apparent reference was. The Logan Act regulates non-governmental negotiations with foreign governments.

The Trump-era Justice Department, after prosecuting Flynn for covering up his policy asks of Kislyak for more than two years, has questioned whether Flynn should have been investigated for a Logan Act violation because prosecuting a crime under the act was unlikely. The DOJ decided this year it wanted to drop the case against Flynn.

Even if Flynn’s case is dismissed immediately, as an appeals court ordered, this latest filing is likely to fuel conservative commentary and theorizing about the early Russia investigation at a crucial time during Trump’s reelection campaign against Biden. Trump and Barr have tried to undercut the Russia investigation, questioning its purpose, dialing back criminal cases brought by Mueller and continuing to revisit its details.

In late April, Trump, Flynn’s legal team and conservative allies seized on the disclosure of a hand-written note from a top FBI official outlining how agents may either refer Flynn for prosecution for illegally negotiating with a foreign government or “get him to lie” or “get him fired.” Trump used the document to argue that Flynn should be “exonerated” and that the charges should be dropped. He also suggested that he’s considering a full pardon for Flynn.

This story has been updated with additional information.

CNN’s Veronica Stracqualursi and Kevin Liptak contributed to this report.