(NewsNation) — When the FBI executed a search warrant at former President Donald Trump’s Mar-a-Lago estate last week federal authorities recovered 11 sets of documents marked as confidential or secret, according to the property receipt from the search.

Although many questions around the investigation remain unanswered — specifically whether Trump himself was the target of the probe — pundits across the political spectrum were quick to highlight similarities, and differences, between the search of the former president’s home and the FBI’s investigation into Hillary Clinton’s emails.

Both investigations are linked to the potential mishandling of confidential information by top officials at the highest levels of government.

In Clinton’s case, authorities were looking at the former secretary of state’s use of a private email account for communication with her staff — some of that correspondence was later found to contain confidential information.

In Trump’s case, the probe stems from boxes of classified documents found at the former president’s Florida home.

Some, including Alan Dershowitz, a renowned attorney and professor emeritus at Harvard Law School, say that comparing the two investigations, and questioning whether the legal process is being applied equally, is appropriate.

“Until (U.S. Attorney General Merrick) Garland fully and specifically answers the hard questions about what appears to be unequal application of rules and practices, ‘what about her emails?’ will be a pertinent question,” Dershowitz wrote in an op-ed for the Wall Street Journal.

Other experts told NewsNation there are stark legal differences between the two cases.

“Whereas Hillary Clinton’s email server never contained properly marked classified information in the various emails received from or sent to unclassified government email accounts, the documents in Donald Trump’s possession were properly marked as classified and continued to have those markings at the time of their seizure,” Bradley Moss, a Washington-based national security lawyer, wrote in an email.

In other words, it’s possible Trump, or someone on his team, knowingly withheld confidential records after being asked to return them in a way that Clinton did not.

That fact may increase the former president’s legal exposure on possible obstruction of justice charges, said Moss.

In fact, the Mar-a-Lago search warrant cited a potential violation of a criminal statute related to obstruction as one of the reasons for seeking the warrant.

“My educated guess is that the Justice Department is looking at a different violation of law in the case of the former president versus Secretary Clinton,” said Jamil Jaffer, the founder and executive director of the National Security Institute at George Mason University.

In July 2016, then-FBI Director James Comey announced the findings from the Clinton email investigation and determined that the former secretary of state was “extremely careless” in her handling of “very sensitive, highly classified information,” but did not find clear evidence that Clinton “intended to violate laws governing the handling of classified information.”

Due to that lack of clear evidence, Comey concluded that “no reasonable prosecutor” would bring criminal charges in such a case and advised federal prosecutors against doing so.

Now, the question of intent may be the key difference between the two investigations.

The search of Trump’s Florida home is just the latest development in a monthslong probe into the former president’s handling of government documents.

In June, one of Trump’s lawyers signed a statement asserting that all classified material at Mar-a-Lago had been returned, according to reporting from the New York Times.

But the FBI’s search last week, which recovered 11 sets of documents marked as confidential or secret, suggests that at least some of the classified material had not been returned.

“The key difference here is likely that with the former president, the Justice Department sought the return of the classified material, putting him on notice that he might be in violation of the law and when they didn’t get it back, they used a search warrant to find and seize it,’” Jaffer said.

It remains to be seen whether Trump, or someone in his circle, could face criminal charges, and details about the specific documents recovered in the search are still unclear.

The former president has denied any wrongdoing and even asked for some of the documents to be returned. His team maintains that, as president, Trump had the authority to declassify any documents he wished to.

On Thursday, the federal judge who approved the search warrant declined to unseal the affidavit, which would reveal the FBI’s explanation for conducting the search.

Instead, Judge Bruce Reinhart will allow the Justice Department until Aug. 25 to provide a redacted version to the court. The judge said there are portions of the affidavit that could be unsealed.