since you're talking about possible security leaks within the country, it would be the job of the FBI so investigate if the question was did the affair involve any leaks of restricted information or security risks. I hear the investigation was more about if his relationship enabled her to access possible sensitive information such as emails, files, or just his computer that she shouldn't have.
Besides, an internal investigation, particularly in a "secret society" environment would be likely to be self censoring or at the least dealing with it all in house and not letting anyone else know. Surely such a secretive organization as the CIA or NSA, etc, would internally generate an attitude that no one outside needs to know anything about internal workings.
In general, any serious risk would be investigated by some group at least a bit outside the ones being investigated.
Supposely the FBI was tipped of a relationship that might question his maintaining security. Once they were tipped, I don't see how they could not investigate it.
Affairs aren't the security risk they were in the past perhaps, just because it's no longer considered outrageous and the chances of successful blackmail over an affair are lower.
The right or wrong of such an attitude is a different debate. It's just a matter of fact that right now the US society is numbed to scandle after so many that such aren't likely to pressure someone in his position to give away information.
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