On Feb. 22, the United States Court of Appeals for the Armed Forces threw out the conviction of an Air Force lieutenant colonel who had sexually assaulted a female enlisted subordinate because the case had been brought long after the expiration of the five-year statute of limitations on military rape cases that was still in effect in 2005, when that assault occurred.

While Congress amended the Uniform Code of Military Justice in 2006 to eliminate the statute of limitations on rape cases, the appeals court ruled that the case against the lieutenant colonel was required to have been brought within the statute of limitations in effect at the time. Nothing in the 2006 amendment or its legislative history suggested that Congress intended to make the change to the code apply retroactively, the court wrote.

The net effect: Only rapes that occurred after Congress changed the military law in 2006 do not have a statute of limitations for prosecution. Those that occurred before the change are still subject to the five-year window. Ms. McSally has not said when she was raped. But based on other details she provided — that she confided to people what had happened only later in her career, after she had been in the military for 18 years, which would have been about 2006 — it appears that the assault she disclosed most likely occurred before Congress changed the law.

The Feb. 22 decision in the case against the lieutenant colonel — who was a captain and an F-16 instructor pilot at the time of the assault — and other recent decisions by the same appeals court have resulted in a number of rape cases being overturned or dismissed, said Don Christensen, a retired colonel who was the Air Force’s chief prosecutor before he left the military in 2014.

For a long time, Mr. Christensen said, the accepted understanding was that there was no statute of limitations in military rape cases. But the recent armed forces appeals court rulings have upended that precedent, he said.

“Cases such as Senator McSally’s are now impossible to prosecute, unless they occurred after 2006,” said Mr. Christensen, who is now the president of Protect Our Defenders, a military victims’ rights group.

The Pentagon did not respond to a query about whether it would appeal the decision to the Supreme Court.