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One employee started to think that move "really is covering up" something related to Clinton's emails.
The emails, which are being investigated by the FBI as part of a broader inquiry into Clinton's private server, were released Monday in a letter from Ron Johnson (R-Wisconsin), the US Senate Homeland Security Committee chairman, McClatchy and other outlets reported.
In March, a US House of Representatives committee requested access to Clinton's server to ensure that she had not deleted any work-related emails.
But her lawyer, David Kendall, told the committee that Clinton aides had changed the server's settings so that only emails she sent and received in the previous 60 days would be saved, according to The New York Times.
And after she left the US State Department, Clinton Executive Service Corp., a company linked to the former US secretary of state, apparently asked the tech firm overseeing her private server, Platte River Networks, to cut the length of time emails were stored to 30 days, according to the emails exchanged between Platte River employees.
"Any chance you found an old email with their directive to cut the backup back in Oct-Feb," one Platte River employee asked another, according to McClatchy. "I know they had you cut it once in Oct-Nov, then again to 30day in Feb-ish."
The employee feared that cutting the backups would make the firm look like it was participating in a cover-up on behalf of Clinton Executive Service Corp., which was footing the bill for its services.
"Starting to think this whole thing really is covering up some shaddy [sic] s---," the employee said in an email to a colleague, according to McClatchy.
"I just think if we have it in writing that they told us to cut the backups, and we can go public saying we have had backups since day one, then we were told to trim to 30 days, it would make us look a WHOLE LOT better," the employee added, according to Politico. "Wonder how we can sneak an email in now after the fact asking them when they told us to cut the backups and have them confirm it for our records."
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The employee's fears evidently stem from the emphasis the FBI has placed on recovering the roughly 31,000 "personal" emails Clinton said she deleted from the server before handing it over to investigators in August.
The FBI has been able to recover at least some of the deleted emails, a source close to the investigation told Bloomberg last month. Intriguingly, agents sifting through the emails Clinton said were "personal" in nature have reportedly handed some over to investigators - indicating that they are relevant in at least some way to the FBI's ongoing investigation.
The optics worsened recently, when the State Department confirmed that Clinton had failed to hand over some work-related emails from her first few weeks as secretary of state, weakening Clinton's promise that her team handed over even more than what was relevant.
In March, Clinton handed over about 30,000 work-related emails for the State Department to make public. Many of the emails contained information retroactively marked "classified" or "top secret," raising questions about what information passed through Clinton's server after she handed it over to Platte River. The company does not have security clearance.
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The investigation into whether Clinton ever mishandled classified information was complicated further when it was revealed last week that her company had hired another firm - Datto Inc. - in June 2013, to store and back up her emails on a cloud in case her server crashed.
Platte River spokesman Andy Boian told Politico, however, that this went against the firm's initial agreement with the Clinton team.
"Datto was never supposed to have a cloud," Boian said. "We specifically instructed Datto to only keep 30 days of information on-site and what they did, against our explicate instructions, was to build a cloud and put this information on a cloud."
Platte River said that, upon learning of the cloud, it "directed Datto to not delete the saved data and worked with Datto to find a way to move the saved information ... back to Secretary Clinton's private server."
In a statement, Datto said it is "working with the FBI to provide data in conjunction with its investigation."