The level of the river Lys rose and the town was embanked. St Nicholas's church too had to be secured.
Crushed stones of demolished parts were used to adapt the floor level (1662).
It is obvious that these infilling layers offered a wealth of information so that the scientists could not resist the temptation to dig off the infillings to the level of the gothic flooring. In that way the broadened bases of the clustered columns were exposed and the archaeological material of earlier days could be dug up. A lot was found, including some brick walls with a polychrome decoration.
The enthusiasm about the exposed medieval floor level was so overwhelming, that - during the works at the choir - it was decided to keep that situation. The Commission for Monuments and Landscapes also advocated that. It settled a discussion which had started at the beginning of this century. As early as the first of May 1907 the President of the Royal Commission had asked to lower the floor level by 130 cm, and that of the nave by 85 cm. The difference in level between the nave and choir, some 0.50 m, which had existed since the 17th century, would in this way be omitted. The plans were designed by architect Geirnaert but they were opposed by a provincial architect and member of the Royal Commission for East Flanders, Valentin Vaerwyck. He favoured an approach of preservation, in which both the interior decoration and furnishing as well as the western portal would be maintained. "To have an idea of the interior architecture I could accept that one side chapel of the northern aisle and a segment of the nave would be restored to their original state" was his advice. There were endless discussions between provincial and national departments of the Royal Commission, which did not benefit the dilapidating church at all.

However, there is more. Although the restored choir has never looked like this in reality, one gets attached to this decoration because it is so unique. The contrast between the serenity of this house of worship and the busy activities at the Korenmarkt has been widely praised. Once you close the door of this plain church you leave the hustle and bustle of the city behind you.

But what a duality ! The austerity clashes with the baroque altars and church furnishing, the paintings, panelling, lecterns and candelabrums that once embodied the catholic revival and are now awaiting their renovation. Once returned to the church, they do not really fit in.
Polished marble panels and epitaphs, baroque altars and elegantly decorated registers are put against a rough facing stone at a much lower level than before. The well-considered proportions and light effects are lost. The tailor-made parcloses and communion rails do not any longer fit the broad column bases. Little is left from the highly-praised integration of plastic arts, where architecture, painting, sculptures, decorations and design are inextricably bound up and run into each other.
By way of compromise the side chapels will get a baroque decoration. The furniture will be presented against walls neutralized by a coating. But what with the interior of the choir ? Its disappeared and damaged stones have been renovated skilfully and with devotion, and no one in his right mind could seriously consider having the immense structure plastered with a smoothing coating. Not only would it be a waste of the community's money, it would also be a failure to appreciate the years of dedication and well-intended craftsmanship.