Thursday was a momentous day for former secretary of state Hillary Rodham Clinton when her chief rival, Bernie Sanders, signaled that he was winding down his primary challenge for the Democratic presidential nomination and President Obama formally endorsed her for president with a laudatory video announcement.

After a long, grueling primary contest, the optics looked great for the now presumptive Democratic presidential nominee and her patron, President Obama – with one exception.

Related: Sanders Wouldn’t End His Campaign, So Obama Just Did It for Him

Clinton is still the target of an FBI investigation into whether she violated federal law by using a private email server throughout her four years as Obama’s secretary of state, even after she and her staff were warned repeatedly that her practice was no longer permitted and that she might be responsible for breach of sensitive or top secret messages.

The Wall Street Journal reported late Thursday that at the center of the Clinton investigation are a series of emails between U.S. diplomats in Islamabad and their superiors in Washington regarding whether to challenge specific CIA drone strikes planned in Pakistan.

The sensitive 2011 and 2012 emails were transmitted via a computer system used for unclassified matters, according to the newspaper. Some of those emails were then forwarded by Clinton’s State Department aides to a private server she kept in New York.

There have been reports suggesting that while she may get a severe slap on the wrist, the Justice Department is highly unlikely to bring charges against her just as her general election campaign against Republican Donald Trump begins to heat up. The State Department Inspector General recently issued a blistering report on Clinton’s mishandling of her email messages – saying that she failed to seek legal approval for her use of a private server and that her action posed “security risks.”

President Obama has repeatedly insisted he has scrupulously stayed out of the federal probe, even while he has done little to hide his determination to help Clinton win the election and preserve his legacy. Obama said during an interview with Chris Wallace of Fox New in early April that “I can guarantee” that the FBI and Justice Department would not protect Clinton while investigating her private emails and server.”

But it might be a challenge for the FBI and Justice Department to turn a blind eye to Clinton’s announcement yesterday, in which he said, “I don’t think there’s ever been someone so qualified to hold this office.”

Related: We Now Know Hillary Lied Multiple Times About Her Email Server

And reporters peppered White House press secretary Josh Earnest yesterday with questions about whether the FBI and Justice Department might be persuaded to go easy on Clinton, now that she has been endorsed by the president.

Asked whether there was a “conflict” in the president endorsing Clinton while the investigation was still going on, Earnest replied, “I believe there’s not.”

“There were a couple of instances when the President was asked about the FBI investigation and in each of those answers, the president made clear that that investigation is one being conducted independent of any sort of political interference. That is the principle to which the president is resolutely committed.”

At one point, Earnest referred to the probe of Clinton’s private emails as a possible “criminal investigation,” which GOP operatives quickly seized on as a serious slip up coming just minutes after the endorsement was announced.

Related: The Strategy that Gave Hillary Clinton the Democratic Nomination

Republican National Committee spokesperson Michael Short issued a statement saying, “The White House’s admission that the FBI is investigating Hillary Clinton’s email server as a ‘criminal’ matter shreds her dishonest claim that it is a routine ‘security inquiry.’”

The question about whether the president could remain impartial and allow the FBI probe of Clinton to proceed unimpeded has been hanging over the high-profile controversy for months. Now it has been greatly magnified by Obama’s endorsement of the former secretary of state and first lady.

The president had been conflicted on the timing of his announcement. As Trump grew in strength, Obama was anxious to get back on the campaign trail and assist Clinton and other Democratic congressional candidates. But he had promised Sanders he would remain officially neutral and on the sidelines until after the primary contests.

The president and Clinton both had to worry about the pace of the FBI investigation and when it was likely to be concluded. FBI Director James B. Comey has said that while the probe was moving along expeditiously, there was no “timetable” for conclusion. Obama and his advisers apparently concluded they couldn’t afford to wait any longer, and the president went ahead with his endorsement of Clinton yesterday.

Related: ‘Crooked Hillary’ Is Still a Better Choice Than ‘Dangerous Donald’

Trump, the bombastic billionaire businessman and presumptive GOP presidential nominee, has been alleging for months that Clinton was being shielded from prosecution by the White House and that the only reason she was “being nice to” Obama was to prevent the FBI from seeking an indictment against her. Shortly after Obama’s announcement yesterday, Trump tweeted: “Obama just endorsed Crooked Hillary. He wants four more years of Obama—but nobody else does.”

Late last month, conservative Rep. Louie Gohmert (R-TX) said in an interview with the Fox Business Network that the Obama administration would never allow Clinton to be indicted “as long as she doesn’t say anything critical of the Obama administration. Gohmert said the investigation of Clinton's use of a private email server should be taken away from the Justice Department and turned over to a special prosecutor.

There are about a dozen FBI agents currently assigned to the case, according to NBC News, as well as a number of Justice Department criminal lawyers. The Associated Press reported recently that the investigation was winding down, and would likely culminate in a sit-down interview with Clinton.

James J. Wedick, a retired FBI supervisory special agent who headed corruption investigations for years in Sacramento said in an interview yesterday that while he believes that Comey and his investigators are relatively immune from political pressure, that may not be the case at the Justice Department, where Attorney General Loretta Lynch and many of the top officials are political appointees.

Related: Most Americans Don’t Believe Hillary Clinton and Donald Trump

“The [FBI] itself is not a political organization, and Comey, while he’s a political appointee, he is in office for ten years, and they’ve done that so the agency wouldn’t be affected by politics,” Wedick said. “However, having said that, the attorney general is a political appointment, she is affected by politics. And prosecutions can only be authorized by the attorney general or a representative of her staff.”

“So therein lies the dilemma,” he said. “It doesn’t bother the agents, it doesn’t bother the men and women working for the FBI, but I imagine it will have something to do with for those over in the Department of Justice who are not career people but are political appointees. So there could be a problem.”

Some legal experts have told the Associated Press that it “appears unlikely Clinton would be formally charged with committing a crime” for using her private email server throughout her four years at the State Department, in contravention of revised rules regulating highly sensitive email transmissions. That’s because the relatively few federal laws governing the handling of classified materials were written primarily to cover spies and leakers. What’s more, prosecutors would have to prove intent to violate the law and expose classified material to hacking, which would be a stretch at best.

Still, there was a definite political downside to the president’s unstinting endorsement of Clinton yesterday with so much uncertainty about the outcome of the federal probe.

Related: 7 Ways Bernie Sanders Transformed the 2016 Election

“Obama legitimately decided to exercise his prerogative as head of the Democratic Party to endorse the person he wants to preserve his legacy,” University of Virginia political scientist Larry J. Sabato said yesterday. “At the same time Republicans will claim this is an attempt to influence the ongoing investigation--though I can't imagine Jim Comey and the FBI will shift whatever course they are on as a consequence. And if Clinton is indicted, the Obama endorsement won't be able to minimize the consequences.”

“But should the entire process be put on hold until the FBI finally decides what it wants to do?” he added. “That is very unwise too.”