The relationship was evidently close enough that both men intervened in a child custody battle involving Kelley's twin sister, Natalie Khawam.
"She is a dedicated mother, whose only focus is to provide the necessary support, love, and care for her son," Allen wrote about Khawam in a Sept. 22 letter to a Washington, D.C., court.
Allen and Kelley communicated often enough over the past two years to produce between 20,000 and 30,000 pages of email and other messages, which were turned over to Defense Department investigators on Sunday.
The actual volume of communications is likely much smaller, an official said, as the printouts include messages involving other people and email threads including prior communications.
A senior defense official told Reuters the messages were seen as inappropriate because they were "flirtatious" in nature, not because they dealt with sensitive information.
But "flirtatious" may be an understatement. Another U.S. official said the Pentagon only decided to refer it for investigation after an initial look found the communications to be of "a sufficient character" to warrant further review.
Allen has denied that the two had a sexual relationship, officials said on condition of anonymity. Adultery can lead to a dishonorable discharge under U.S. military law.