U.S. Gen. John R. Allen and U.S. Gen. David H. Petraeus walk into the July 2011 ceremony at which Allen took over for Petraeus. (Chairman of the Joint Chiefs of Staff/Flickr)

White House spokesman Jay Carney declined to comment on the status of the CIA Director position vacated by Gen. David Petraeus or Afghanistan commander Gen. John Allen, saying only that the president had "faith" in Allen to continue his duties overseeing troops in the Middle East while under investigation.

"There are processes in place to deal with these sorts of things," Carney said.

Allen was expected to return to Afghanistan on Saturday, CBS reported.

The latest detail in the "love pentagon" that includes Carney and Allen came Tuesday morning when the New York Post reported that the two military commanders wrote letters supporting Jill Kelley's twin sister in a custody battle regarding her four-year-old son. Both Petraeus and Allen asked a judge during the past two months to overturn a ruling denying custody of the boy to Natalie Khawam because of concerns about her mental stability.

Kelley is said to have written emails to Paula Broadwell, Petraeus' former mistress, complaining about Broadwell flaunting around military bases. Kelley also is said to have had inappropriate "flirtatious" email exchanges with Allen.

Carney said the White House learned about the Petraeus investigation on Wednesday -- two days before Petraeus resignation was accepted -- and of the Allen investigation on Friday -- two days before Defense Secretary Leon Panetta said he heard about it.

Allen replaced Petraeus as the leader of American forces in Afghanistan in July 2011. He was on course to become the top commander in Europe of U.S. and NATO forces, but Panetta put that nomination on hold early Tuesday.  Allen's successor in Afghanistan, Gen. Joseph Dunford, will be considered by lawmakers this week.

Though Petraeus escaped prosecution by virtue of being outside of the military, Allen still faces court martial if a Defense Department investigation concludes he had an affair with Kelley. Adultery is prohibited by military rules.

More on the Petraeus scandal here.

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