Aides to Hillary Clinton were on high alert in January 2011.

Justin Cooper, the man who oversaw the secretary of state's home-based email servers, sent a warning to Huma Abedin.

"I had to shut down the server. Someone was trying to hack us and while they did not get in i didnt want to let them have the chance to. I will restart in the morning," Cooper said in a 2:57 a.m. email.

"Omg," Abedin replied at 7:05 p.m., using the shorthand for "Oh my God."

Early the next morning, Abedin wrote to State Department officials Jake Sullivan and Cheryl Mills, Clinton's chief of staff: "Don't email hrc [Hillary Rodham Clinton] anything sensitive. I can explain more in person."

The sense of alarm among Clinton's staff appear in partially redacted documents released by the FBI this week that were part of the bureau's "Midyear Exam" investigation, which looked into Clinton's mishandling of classified information on her unauthorized private email server while serving as secretary of state.

In handwritten notes of an interview in March 2, 2016, FBI agents wrote that Cooper asserted a hack was "never confirmed."

But the debate over whether Clinton's server in the basement of her home in Chappaquiddick, N.Y., remains alive today. During a hearing with Attorney General William Barr this week, Rep. Louie Gohmert accused FBI Director Christopher Wray of a pro-Clinton cover-up by not pressing the intelligence community for proof that it was not hacked by China.

This follows reporting last fall that a Chinese company succeeded in hacking the server. The Daily Caller News Foundation reported the firm, located in the Washington, D.C.,-area, had access to Clinton's emails in real time courtesy of a code embedded in the New York-based server which then made copies of the emails, some of which contained classified information. The FBI responded by saying there was no evidence that Clinton's private server was hacked.

Still, a source told Fox News that the Intelligence Community Inspector General, which found the breach via metadata, was so alarmed by the breach that it notified the FBI, including Peter Strzok, who led the Clinton emails investigation and briefly special counsel Robert Mueller's Russia investigation. Strzok was pushed out of Mueller's team and later fired by the FBI after it was discovered he exchanged anti-Trump text messages with ex-FBI lawyer Lisa Page, with whom he was having an affair.

The new tranche of FBI documents also reveal what appear to be glaring security oversights when it came to Clinton's servers.

The FBI's handwritten notes show Cooper discussing the use of a “SCIF," or sensitive compartmented information facility, in Clinton's homes in Chappaqua and Washington, D.C.

Although "phone/fax/video" were checked off as "secure" in the residences, the notes said the server rooms were sometimes left vulnerable. “Open door — not always secured, sometimes when HRC not @ residence was not closed. (both resid)," the notes said.

The notes also said there were "home computers," not "secure computers."

The newly released FBI records also show that some of the Clinton-related investigative information has been damaged or lost. One declassified FBI document from Feb. 12 says that notes that were taken by special agents on Aug. 3, 2015 were nowhere to be found, saying, "On or about February 4, 2019, Special Agents [redacted] attempted to locate [redacted], described as 'Notes from Meeting' acquired by [redacted]. The Special Agents looked through all case materials in the CI-13 file and workbox area, however, they were not able to locate this item."

"As such, [the FBI's Washington Field Office] CI-13 considers the item missing and will enclose this document into 1A4 as a placeholder until the missing item is located," the FBI said.

Another declassified FBI document, also from Feb. 12, said a CD with Clinton investigation materials on it had been cracked and damaged beyond repair: "Special Agent [redacted] attempted to copy the damaged CD at the WFO Computer Analysis Response Team self-service area, but was not able to do so. Special Agent [redacted] spoke with the FBI information technology specialists on the ground floor of [the FBI's Washington Field Office] regarding the damaged CD, who indicated it was unlikely the CD could be copied.”

The FBI investigation into Clinton's emails came to a conclusion during the 2016 presidential election. Former FBI Director James Comey publicly recommended in 2016 that no charges be brought against Clinton, who was then a candidate for president, but admonished Clinton and her colleagues for being "extremely careless" in handling classified information.

One of the main controversies stemming from Clinton's emails was how a technician managing the server deleted 33,000 emails. The FBI was only able to recover about 5,000 of the emails, which were released in tranches up until earlier this year as part of a Judicial Watch lawsuit. Clinton has said she "never received nor sent any material that was marked classified," but the FBI found 110 emails did contain classified information.