Restorers have found two concealed windows in the dome of St Catherine of Italy's church in South Street, Valletta.
The windows were revealed during a thermographic analysis of the church, which was conducted to better understand the material and technique used during its construction.
The restoration project, which is now in full swing, was commissioned to the internationally acclaimed Italian company Giuseppe Mantella Restauri and was sponsored by Bank of Valletta.
The church has endured centuries of exposure to the natural elements, rainwater, damage suffered during the war as well as seismic activity.
The paintings were consequently detached from the limestone and, to reattach them, a special material, a consolidant, had to be injected behind them to stick them to the stone again.
"In some places, the layers of paint are so fragile that a layer of special tissue paper is attached to an area of the painting to prevent it from crumbling to pieces during the injection of the consolidant," said restorer Giuseppe Mantella.
"Consolidation is the first and often hardest step when dealing with the restoration of an artefact especially when it has been damaged through the passage of centuries."
He said the scientific analysis revealed a complex stone structure that had undergone a lot of modifications during its lifetime.
Historical research was a very important step that brought to light techniques of past restoration interventions, helping the restorer to better understand the techniques and consequently to formulate the proper methodology of restoration, he said