EXCLUSIVE: An intelligence community review has re-affirmed that two classified emails were indeed “top secret” when they hit Hillary Clinton’s unsecured personal server despite a challenge to that designation by the State Department, according to two sources familiar with the review.

The sources described the dispute over whether the two emails were classified at the highest level as a “settled matter.”

The agencies that owned and originated that intelligence – the CIA and National Geospatial-Intelligence Agency or NGA – reviewed the emails to determine how they should be properly stored, as the State Department took issue with their highly classified nature. The subject matter of the messages is widely reported to be the movement of North Korean missiles and a drone strike. A top secret designation requires the highest level of security, and can include the use of an approved safe.

The sources, who were not authorized to speak on the record, told Fox News that while the emails were indeed “top secret” when they hit Clinton’s server, one of them remains “top secret” to this day -- and must be handled at the highest security level. The second email is still considered classified but at the lower “secret” level because more information is publicly available about the event.

The findings have been transmitted to the State Department, which continues to challenge the intelligence community’s conclusions about the classification of all the emails. But the department has no authority to change the classification since it did not originate the information.

On Nov. 6, Politico reported that the intelligence community was retreating from the “top secret” classification, a development that could have helped Clinton’s presidential campaign deflect allegations about mishandling classified material. Fox News can confirm it is true the handling of one email has changed since it was drafted and sent, but this change has no bearing on the “top secret” nature of the emails when first received on Clinton’s server. And this is what matters to the FBI probe.

While the classification finding is important, the central issue is whether the FBI investigation concludes there was or was not a criminal violation.

Fox News reported earlier this month that two top Republican senators have written directly to Secretary of State John Kerry and Director of National Intelligence James Clapper about possible leaks from their departments on their review of Clinton’s emails -- wrongly leaving the impression that the two “top secret” messages were not that sensitive.

The letter was sent by Republican Sen. Bob Corker, who chairs the Foreign Relations Committee, and Sen. Richard Burr, who heads the powerful Intelligence Committee, on Nov. 13, with copies sent three days later to the intelligence community and State Department watchdogs known as inspectors general. The IGs were asked to conduct an independent review of the process.

While the senators’ letter is not public, Fox News has confirmed that the senators cited the Politico report from Nov. 6 where unnamed sources claimed the two “top secret” emails had been downgraded after a second review. While hailed by Clinton’s supporters as evidence she did not break the law and send classified information on her personal email account, the Politico story was later updated to reflect the fact that Clapper’s office said the review was ongoing.