ERIC FEFERBERG / AFP / Getty Images Malian soldiers enter the historic city of Timbuktu on Jan. 28, 2013

The preservationists of Timbuktu’s centuries-old artifacts have been holding their breath for weeks, waiting for the moment when the French military would seize back Mali’s ancient northern capital from the Islamic militants who have occupied it for 10 months. At stake were the city’s most precious treasures: tens of thousands of centuries-old, priceless calligraphed manuscripts, whose fate under the jihadists’ rule was deeply uncertain.

On Monday, that moment finally came — and by nightfall, the state of Timbuktu’s treasures was as confused as it had been before.

(MORE: Why Islamists Want to Destroy Timbuktu’s Treasures)

When Malian and French soldiers rolled into town in armored vehicles early Monday, they found what the preservationists had most dreaded: Timbuktu’s new Ahmed Baba Institute, an expensive adobe construction opened in 2010 — the city’s splashiest international project in years — had been torched by militants of al-Qaeda in the Islamic Maghreb last Thursday as they prepared to flee the French advance. From Bamako, Timbuktu’s Mayor Hallé Ousmane Cissé, who had fled his city nearly four weeks ago, told journalists that the militants had burned the center’s collection of about 40,000 ancient manuscripts, some of the 300,000 or so historic documents stashed in libraries in Timbuktu and the villages around it, mostly as family heirlooms. “The manuscripts were a part not only of Mali’s heritage but the world’s heritage,” Cissé told the Guardian. “By destroying them, they threaten the world. We have to kill all of the rebels in the north.” Reporting from inside the Timbuktu building itself, Sky News correspondent Alex Crawford told viewers that the jihadists had destroyed the center’s contents. Meanwhile, Cissé was quoted on the network’s website as saying, “They torched all the important ancient manuscripts.”

That is not so, according to those who’ve worked for months to keep the documents safe.

In interviews with TIME on Monday, preservationists said that in a large-scale rescue operation early last year, shortly before the militants seized control of Timbuktu, thousands of manuscripts were hauled out of the Ahmed Baba Institute to a safe house elsewhere. Realizing that the documents might be prime targets for pillaging or vindictive attacks from Islamic extremists, staff left behind just a small portion of them, perhaps out of haste, but also to conceal the fact that the center had been deliberately emptied. “The documents which had been there are safe, they were not burned,” said Mahmoud Zouber, Mali’s presidential aide on Islamic affairs, a title he retains despite the overthrow of the former President, his boss, in a military coup a year ago; preserving Timbuktu’s manuscripts was a key project of his office. By phone from Bamako on Monday night, Zouber told TIME, “They were put in a very safe place. I can guarantee you. The manuscripts are in total security.”

In a second interview from Bamako, a preservationist who did not want to be named confirmed that the center’s collection had been hidden out of reach from the militants. Neither of those interviewed wanted the location of the manuscripts named in print, for fear that remnants of the al-Qaeda occupiers might return to destroy them.

(MORE: The history of Timbuktu, an Ancient Cultural Crossroads)

That was confirmed too by Shamil Jeppie, director of the Timbuktu Manuscripts Project at the University of Cape Town, who told TIME on Monday night that “there were a few items in the Ahmed Baba library, but the rest were kept away.” The center, financed by the South African government as a favored project by then President Thabo Mbeki, who championed reviving Africa’s historical culture, housed state-of-the-art equipment to preserve and photograph hundreds of thousands of pages, some of which had gold illumination, astrological charts and sophisticated mathematical formulas. Jeppie said he had been enraged by the television footage on Monday of the building trashed, and blamed in part Mali’s government, which he said had done little to ensure the center’s security. “It is really sad and disturbing,” he said.

When TIME reached Timbuktu’s Mayor Cissé in Bamako late Monday night, he tempered the remarks he had made to journalists earlier in the day, conceding in an interview that, indeed, residents had worked to rescue the center’s manuscripts before al-Qaeda occupied the city last March. Still, he said that while many of the manuscripts had been saved, “they did not move all the manuscripts.” He said he had fled earlier this month after living through months of the Islamists’ rule, a situation he described as a “true catastrophe” and “very, very hard.” He said he expects to fly back home by the weekend on a French military jet. By then, perhaps, the state of Timbuktu’s astonishing historic libraries might be clearer.

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