The Air Force has decided not to charge a colonel accused of sexually abusing two boys

Where do you find that? I haven't seen that in anything searching it.
"Air Force Col. Eric Holt, 48, was accused of sexually assaulting a young child in 2016 while he was working as an anesthesiologist at the Uniformed Services University of Health Sciences. According to documents from the case, reported by USA Today, an elementary-school-aged boy told his mother and two other witnesses that Holt raped him, and he had physical injuries from the abuse."

"In October 2016, allegations of sexual abuse arose after one of the boys returned from a visit with Holt. The boy awoke the night of Oct. 13 having soiled himself, according to the June 14 memo to Maj. Gen. James Jacobson, the officer deciding whether Holt would be charged.

As his mother cleaned him up, the boy told her that Holt "pulls on his penis and puts his fingers in his bottom." Crying, he told two other women in the home the same story. A photo of his bruised penis and a statement from one of the women were left out of the investigative report by the Air Force, according to the memo.

The memo catalogs other forms of abuse the boys allegedly suffered at the hands of Holt, including black eyes and facial bruising. They also cite the opinion of a licensed psychologist, who found the boys to be credible."

How does this have to do with a custody fight when it doesn't sound like it was his child or children?

I found a custody modification in 2016 - divorce was in 2014. They were married in 2005. She thought about filing for divorce in 2009 but didn't and after he got injured flew to be with him. They were having issues because of deployments and he didn't want kids. They had premature twins in 2011. "Martial discontent continued, and on October 9, 2013, the parties entered into a “Marital Separation and Custody Agreement and Child Support Term Sheet.” The agreement addressed custody, visitation, and support. It provided a phase-in access schedule for the Father for the first 90 days, after 90 days until 120 days, from 120 days until the Twins are four years old, and then after the Twins turn four in October of 2015."
https://mdcourts.gov/sites/default/files/unreported-opinions/2017/1015s16.pdf
Based on that it sounds like he was painting mom in bad light and the court found no material change to modify custody. I see nothing about false sexual assault allegations and how it had anything to do with his divorce (that happened before these boys came forward).

https://www.leagle.com/decision/inmdco [login to see] 9

Well the article makes it seem like two different children and not his kids because it says one reported it after being seen by him in a doctor capacity. So it's very strange.