A legal organization dedicated to religious freedom is demanding the Air Force reverse its position after a two-star commander reopened an investigation into accusations against a subordinate — accusations that were investigated and not substantiated more than two years before at another base.

Then, without any new evidence, the commander nevertheless decided to punish that subordinate.

First Liberty Institute says Col. (Dr.) Michael Madrid was denied due process and also may have suffered discrimination because of the two-star's actions.

Michael Berry, senior counsel and director of military affairs at First Liberty, said he was surprised to learn of the June 2016 decision of Maj. Gen. John McCoy, then the acting vice commander at Air Education and Training Command at Joint Base San Antonio-Randolph, Texas, to issue Madrid a Letter of Admonishment.

"I am a former active-duty Marine JAG, and I've dealt with numerous military investigations and issues like this, and I've never seen anything like this happen," Berry said. "I know of no legal authority that gives a commander the ability to, essentially, reopen a cold case or a closed file like this. The two-star … gave no indication of how he became aware of this, or what gave him the authorization to reopen the investigation, or to take the action he took. That's why we believe this is a violation of Col. Madrid's due process."

In 2014, Madrid, then a lieutenant colonel with more than 20 years in uniform, first as a naval aviator and then as an Air Force doctor, was investigated at F.E. Warren Air Force Base, Wyoming, for allegations that he had made "derogatory or demeaning comments about homosexuality." The airman who made the claim, whom Madrid had mentored, was facing court-martial for serious offenses, and Madrid had been listed as a potential witness in the case.

Col. Hans Ritschard, then commander of the 90 th Medical Group initiated a command directed investigation into the allegations of unprofessional conduct.

Madrid denied the allegations.

"Col. Madrid stated he is a devout Christian with sincerely held religious beliefs, and that his treatment of others does not change based on their religious belief, or lack of belief, or their sexual orientation," Berry wrote in his March 29 demand letter to the current vice commander at AETC, Maj. Gen. Mark Brown. "Multiple witness statements included in the CDI deny observing or hearing Col. Madrid make derogatory or demeaning comments about homosexuality.

"Multiple witness statements also make reference to Col Madrid's religious beliefs as a possible basis for the allegations in the CDI."

In an interview, Berry said that Madrid discussed his religious beliefs, including his views on homosexuality and marriage, if asked, but did not foist them upon others.

"The culture in the military has become far more politically correct, far less tolerant of people of faith, and the expression of religious beliefs," Berry said. "So the colonel, he is obviously aware of that, and would only have those conversations when people would ask him.

"But when people do ask him questions about his faith, he is not ashamed of it, he doesn't hide it, and to that extent people in his unit, people who work with him, are aware that he is a Christian and that he holds to those Biblical beliefs, those religious beliefs."

The CDI was completed in April 2014, with the investigator concluding that the allegations against Madrid were unsubstantiated.

Madrid subsequently moved to Randolph, where he received a Meritorious Service Medal for "singularly distinctive achievements."

Then the roof caved in.

On June 29, 2016, more than two years after the CDI was closed, McCoy issued the Letter of Admonishment to Madrid, based on the same allegations that the CDI failed to substantiate. McCoy concluded that Madrid lied to the investigating officer when he denied the allegations against him.

"Specifically, Maj. Gen. McCoy alleged that Col. Madrid "breached integrity by giving the impression that [he] had not made those comments," Berry wrote in the demand letter. "As a result, Maj. Gen. McCoy’s LOA resulted in a [Unfavorable Information File] being placed in Col Madrid’s record — a potentially career-ending action."

McCoy never talked to Madrid before taking the action against him. "He was completely blindsided," Berry said.

In his demand letter, Berry said the actions taken against Madrid violate federal law and Department of Defense and Air Force regulations, and they deprive Madrid of due process.

"These adverse and potentially career-ending punishments should be rescinded and removed from Col. Madrid’s service record," he wrote.

In a March 30 emailed response to questions about the case, Capt. Jose Davis, a spokesman for AETC, said the command is "aware of Col. Madrid’s situation and his retention of legal representation."

"Maj. Gen. Mark Brown, Vice Commander of Air Education and Training Command, received a letter on March 29, 2017, from Colonel Madrid's legal representation. We are now working through the process of verifying the facts around Colonel Madrid's protestations," he wrote.

"We thoroughly review all instances, to include this one, in which the Air Force's neutrality toward religion is questioned. The Air Force is dedicated to creating an environment in which people can realize their highest potential without any consideration of their personal religious or other beliefs. Leaders must ensure their words and actions cannot reasonably be construed to be officially endorsing or disapproving of any faith, belief, or absence of belief. Mutual respect is an essential part of Air Force culture."