Patricia O’Kane-Trombley woke up Monday with a bad cold and, as she said, “put life on hold.” That meant no answering the phone.

But why, she wondered, did the people from Dover Air Force Base keep calling?

When she finally returned their call Tuesday morning, they had disturbing news. A bag with a 4-inch piece of flesh had gone missing from Dover’s mortuary, which handles the remains of the fallen from Iraq and Afghanistan.

The missing flesh could have belonged to her son, Air Force Capt. Thomas J. Gramith or his friend, Capt. Mark R. McDowell. Both men were killed in July, 2009 when their F-15E fighter jet crashed in Afghanistan. The mortuary wasn’t sure. But what they did know was that the plastic bag that was supposed to contain it was empty.

The missing flesh was part of a series of problems that federal investigators uncovered at the Dover mortuary after whistleblowers reported that remains were being mishandled and that there were not enough safeguards in place to prevent mishaps. Family members and members of Congress reacted angrily to the news and have called for further investigation.

If she had heard the news in the days immediately following her son’s death, O’Kane-Trombley “might have screamed and yelled at them.” But she’s made peace with her son’s death and life.

“A lot of me is full with intense pride for both [airmen] for what they accomplished in their short lives,” she said by phone from her home in Colorado Springs. “I don’t like mix-ups. Don’t get me wrong.”

Stan McDowell, Mark McDowell’s father, got the call on Saturday.

“They were very apologetic, and it was all heartfelt,” he said. “We know Mark was a Christian, and that he’s in heaven. So we look at it like — ok, so maybe there are some remains that did not end up in his burial site. Or maybe it did. Or maybe it ended up in Thomas’ location. That’s not really a concern to us. And the reason is: we know Mark is separated from his body, and that he’s in heaven.”

The two men are buried together, with a shared headstone, at Arlington National Cemetery. Initially, Gramith, who was 27, was buried in Minnesota, where he grew up, his mother said. A few months after their deaths, the military contacted the families and said they had recovered additional remains but, given the nature of the crash, they could not tell which belonged to Gramith and which were McDowell.

Gramith was then moved from Minnesota to Arlington where he was buried alongside McDowell, 26, who grew up outside of Charlotte, N.C. and the additional remains.

Both families said they were assured by the Air Force’s promises to ensure that something like this never happens again.

That would be the thing Gramith would focus on, his mother said: “If Tom were here he’d say, ‘What can we do to make this better?’”

Staff researcher Magda Jean-Louis contributed to this report.