BENOIT TESSIER / REUTERS A museum guard picks up boxes holding ancient manuscripts, which were partially damaged by Islamist rebels, at the Ahmed Baba Institute in Timbuktu on Jan. 31, 2013

One week after Islamic militants fled Timbuktu under French bombing strikes, preservationists are deeply uncertain about how to continue protecting the city’s priceless ancient documents — a conundrum that cuts to the heart of how treasures are safeguarded through political upheaval in places where locals have little trust in government.

When French and African forces rumbled into northern Mali’s ancient capital 10 days ago, Timbuktu’s mayor, who had little direct information, told journalists erroneously that the jihadists had destroyed “all the important documents” and that Malians needed to “kill all the rebels.”

In fact, Timbuktu’s residents and preservationists had told TIME early last year that they had rescued tens of thousands of manuscripts before the militants seized northern Mali. They agreed to talk on the condition that TIME kept their secret until the jihadists had been defeated. The operation was conducted by Timbuktu’s old families, which have looked after the city’s 300,000 or so ancient documents for centuries. The residents left behind just a few hundred manuscripts in Timbuktu’s only publicly run collection, the Ahmed Baba Institute, in order to conceal the fact that they’d hidden the bulk of them elsewhere; it was those that were destroyed last month.

(MORE: Mali: Timbuktu Locals Saved Some of City’s Ancient Manuscripts from Islamists)

Even jihadists who are illiterate are likely aware of the manuscripts’ high value, given the headline news generated by their potential destruction. Timbuktu’s libraries comprise one the most detailed written accounts of Africa, from when the city was a gold- and salt-trading hub in the 15th and 16th centuries with a thriving community of scholars and several universities. When TIME visited Timbuktu in 2009 to describe the manuscripts, residents explained that each family appointed one of their children to look after the documents for the next generation — a system that has lasted through countless migrations, invasions and skirmishes over the years.

But with the manuscript pages brittle — they can crumble at the lightest touch — preserving them has become urgent. Not only are they fragile, but they might be especially vulnerable during Mali’s unsettled conflict, since such periods of upheaval often lead to the looting and trafficking of historical treasures. Preservationists also fear that as young Malians become more mobile they might sell them, especially as foreign collectors have begun scouting for treasures in Timbuktu during the past decade. Until very recently, Mali had no law forbidding the manuscripts from leaving the country, and in any case, the government had little means to stop them.

Changing this will not be easy. To the frustration of preservationists, only about 10% of Timbuktu’s documents are housed in the government-run Ahmed Baba Institute, a modern adobe-style building sponsored by the South African government in 2009, which has the city’s only state-of-the-art digitizing equipment. The families have had no confidence in anyone but themselves looking after their collections. International organizations have found locals extremely reluctant to give their manuscripts over for safekeeping or even to loan them for brief periods to be digitized.

With the war over in Timbuktu, now comes the question of what to do next. “We’ll do everything possible to look at how the originals can be more securely safeguarded,” Irina Bokova, Director General of UNESCO, said in an e-mail to TIME on Monday. Bokova flew to Timbuktu on Saturday with French President François Hollande and believes it is urgent to tackle the state of the manuscripts. “If there is no digital copy, they could be lost forever,” she wrote in her e-mail. “Given that the vast majority of the Timbuktu documents are held in private collections, this situation presents a particular challenge. We must work with these communities in Timbuktu to find a way forward.”

(MORE: For the Treasures of Timbuktu, a Moment of Grave Peril)

Ultimately, the key to preserving Timbuktu’s manuscripts may lie not with organizations like UNESCO but with Mali’s bitterly divided politicians.

So long as the government in Bamako’s present dysfunction continues — and it remains estranged from the largely ethnic Tuareg population of the north — the collections will be vulnerable, say some experts. The 30 to 40 Timbuktu families who have been custodians of the manuscripts have lived through centuries of tension and alienation from Mali’s government in Bamako, which has in turn invested little in the far poorer desert region of northern Mali. To them, it has seemed better to keep the manuscripts hidden in rickety closets or under floorboards at home, rather than hand them over for safekeeping to an unstable government, which collapsed after a military coup last year. “You are not going to solve the question of the manuscripts without solving it politically,” says Shamil Jeppie, director of the University of Cape Town’s Tombouctou Manuscripts Project, which has helped coordinate the preservation work. “There is no sense in trying to protect the manuscripts if you don’t properly protect the city.”

Though the idea seems unbelievable now, Timbuktu’s residents initially wanted Ahmed Baba to have free access, with no security, much like a public library in any city. “The building was conceived with no walls around it so people could walk right in from the street or the square outside the mosque,” Jeppie says. Even though the government finally walled off the compound, it was not heavily secured. By the time militants seized Timbuktu last March, he says, “there was a simple night watchman.”

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