Chartres cathedral is being restored to its original painted glory – but some of its mystery may be wiped away.

We scrambled through the scaffolding, high up into the choir 200 feet above the ground, to see the progress on the first stage of the restoration, which is to be unveiled just before Christmas. Conservation experts have stripped away the patina of the centuries to uncover a pale ochre wash, brushed on to the walls when the cathedral was constructed between 1194 and 1225. Still almost complete is the original white pattern of "fake" stone joints, which do not follow the lines of the real masonry. They were painted on to give the walls a more uniform look.

The soaring arches, ribs and columns – the vaulting which made the immense Gothic cathedrals possible – have been scrubbed from their unsavoury, deep grey to the original bony white. The elaborately carved keystones which hold the vaulted roofs together have been repainted to a gleaming red, green, black and gold, based on the fragments of medieval colour which have survived.

With €6m of European, French state and local government funding, work will begin on other parts of the cathedral next year, and should be complete by 2014.

"You could say that we are taking a risk by transforming something which is admired and loved by so many people," said Gilles Fresson, the historian overseeing the work for the rectorate of Chartres cathedral. "But you could also say that we are putting our trust in the people who first conceived this beautiful place.

"People sometimes think of Gothic architecture as dark and sombre, but that is not the way that the original architects and masons saw their work. Cathedrals were originally intended as a way of gaining a glimpse of paradise on earth. They were designed to be ethereal buildings, temples of light."

Mr Fresson expects some visitors to Chartres to be taken aback – maybe even angered – by the transformation. "There is no doubt that we will lose something, even if we gain a great deal," he said. "The sense of mystery, the sense of the passing ages, which you receive when you enter the dark interior of today will be replaced by something fresher and much more dynamic."

Concerns have been expressed, in particular, about the effect of the restoration on Chartre's exquisite stained-glass windows: the most complete, and to many people the most beautiful anywhere in the world. The glass is also being gradually restored, largely with money raised by charitable appeals

"You could argue that the power of the windows has been increased by the cathedral's dark interior and that their beauty will therefore suffer," said Mr Fresson. "Our first impression, from the work so far, is that the effect will be different, but no less beautiful."

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With the help of a powerful torch, he took us on a tour of the darkened recesses of the cathedral, pointing the beam at the still unrestored key-stones high in the roof, picking out the tiny flecks of medieval colour which still remain. He also took us to see a recently restored group of 13th-century statues above the western door of the building. Here too, the recent removal of centuries of grime has shown that, as long suspected, the statues adorning the exterior of Gothic cathedrals were once brightly painted. Scraps of blue, black and green have reappeared on the cloaks or faces of the biblical figures. Entire statues have been shown to be not plain stone but dyed in the same ochre "sizing", or wash, as the interior walls.

"Of course, some people will complain when the interior is restored," Mr Miller said. "People always complain. They complained when these statues were restored. They complained when Rembrandt's Night Watch was restored and turned out not to be an image of the Night Watch at all. Personally, I can't wait until the inside of the cathedral is cleaner and brighter. We know that that was how it was meant to be. Why should it not be that way again?"