The project has so far included the dangerous task of clearing unexploded mines and shells from the seafront site and scouring the northern Jaffna peninsula for scarce limestone bricks to use for the rebuilding.
Sri Lanka's separatist Tamil rebels laid siege to the European-built fort, branded a symbol of colonial oppression, during the conflict that raged on the island until 2009.
"There was damage due to the war. Artillery fire and things like that," Mandawala, who is heading the mammoth restoration of the 17th-century complex.
"Then there was also vandalism. Some people whose houses were damaged during the war had vandalised the fort to remove limestones to rebuild their homes."
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When the Dutch and British ruled Sri Lanka in the 1600 and 1700s, the fortress was a sign of European military might in the Indian Ocean region, a star-shaped structure with moats and draw bridges.
But it was the Portugese who originally built on the site, 400 kilometres (250 miles) north of Colombo, constructing a small garrison after capturing the region in 1619.
The British, who expelled the Dutch in the late 18th-century, added a stately residence for its governor who was based in Jaffna, then the gateway to Sri Lanka.
Hundreds of years later after Sri Lanka gained independence, the fort came under attack from Tamil rebels, fighting for a separate homeland for the island's ethnic minority.
Rebels went on the rampage to successfully recapture the fort from Sri Lankan troops who occupied the site after Indian forces exited the conflict in 1990.
"They wanted to prevent the Sri Lankan military getting control of the fort which was a staging post for attacks in the past," Tamil legislator from Jaffna, Dharmalingam Sithadthan, told AFP.