Three New York firefighters raise an American flag amid the rubble of the World Trade Center on Sept. 11, 2001. (Thomas E. Franklin/Bergen County Record)

To our most sacred and uplifting media moments we must often add a later, follow-up period of difficult questions and even debunking, which brings me to this:

Does it matter to you that the American flag raised by three weary firefighters at Ground Zero on the afternoon of Sept. 11, 2001, has gone missing? Does it matter that the flag that toured the world at benefit concerts and aboard Navy ships en route to war — bringing people to tears wherever it went as they touched it and saluted it with holy reverence — was, in fact, not the same flag that was in the unforgettable news photo of that moment, even though everyone was told that it was?

In Michael Tucker and Petra Epperlein’s stirring and even baffling CNN documentary “The Flag” (airing Wednesday night), we are taken along on a hunt to solve a mystery (What happened to that flag? Who has it?) but also to look within ourselves at the mysterious processes of catharsis and symbolism. (In other words, why did we need that flag to do what it did to us emotionally?)

“The Flag” is precisely the sort of film we should be making and watching at this particular distance from the attacks. Enough years have gone by that we can — tenderly, perhaps still cautiously — reexamine our emotions and responses without setting off a screaming match about patriotism. Tucker and Epperlein try to retrace the iconic appearance and then disappearance of what is arguably one of the 9/11 era’s most treasured artifacts.

What is known: On the morning of the World Trade Center attack, the flag in the picture was hanging on the pole of a yacht moored at a small marina just west of the Lower Manhattan site. The yacht belongs to Shirley Dreifus and Spiros Kopelakis. At some point in the afternoon, a group of New York firefighters removed the flag and carried it to the still-smoking rubble, where they raised it. This was captured by several photojournalists on the scene, and none caught it more perfectly than Thomas Franklin, who was shooting for the Record newspaper of Bergen County, N.J. Within 24 hours, his picture was displayed around the world. The image became posters, lapel pins, T-shirts, sculptures, quilts.

Although Franklin declined to be interviewed, the filmmakers talked to just about anyone they could find who was there. The moment the flag was raised is compared to the famous photograph of World War II Marines raising the flag at Iwo Jima (itself a re-creation of a moment). Former New York mayor Rudy Giuliani says the picture was nothing short of salvation for a wounded city and nation, a symbol of American perseverance.

Dreifus and Kopelakis recount their misadventures in bureaucracy when, after an appropriate interval, they asked for their flag back so they could donate it to the Smithsonian. A flag was indeed returned to them, having been signed by politicians, celebrities, troops and firefighters — but it was twice the size of the flag from their boat and noticeably larger than the flag in the photograph.

The sleuthing that follows in “The Flag” (which is based on a book by David Friend) strikes the right balance between puzzlement and outrage. Clue by clue — after they’ve examined video footage from the Ground Zero aftermath — the filmmakers discover that someone had taken the flag away as early as that first night. Giuliani staffers procured what they believed to be the Ground Zero flag several days later for a ceremony at Yankee Stadium, and it then went on a highly publicized world tour. Did officials know then that it wasn’t really the flag?

This is where “The Flag” does its best and most subtle work: If it wasn’t really the flag, was the substitute just as meaningful? At our patriotic core, the reflexive answer is yes. But if truth is also a founding principle, then there’s a gnawing dissatisfaction with this implicit ruse. And, given the war we still fight in response to Sept. 11, there’s an uncomfortable metaphor in the central narrative of “The Flag,” suggesting that nothing was what it seemed.

The Flag

(90 minutes) airs Wednesday at 9 p.m. on CNN, with encores.