Reconstruction of historic building elements is often necessary in adaptive re-use projects. Optimally this is performed with as much original material as can be salvaged. However, the use of hydraulic lime mortars with no cement content in reconstructed masonry can lead to long curing time and excessive deformation under mechanical loads. Therefore, local masonry reconstruction in adaptive re-use projects using historic materials that need to adhere to pressing construction schedules should always be closely monitored. The objective of the paper is to demonstrate the need for accurate geometric survey of vault structures in order to achieve accurate deformation results using numerical analysis. Focusing on a complex reconstruction project involving a masonry vault at the Royal Academy of Fine Arts in Ghent, practical aspects of damage monitoring, geometric survey and computational analysis of historic structures are jointly presented and addressed. The vault was dismantled and reassembled using the original bricks and a newly made hydraulic lime mortar, the latter of which was mechanically characterized. Existing cracks in the masonry walls supporting the vault were monitored for the detection of new damage. Detailed geometric surveys were carried out using terrestrial laser scanning at two points in time after the reconstruction of the vault: a) before the removal of the formwork and b) after the removal. These scans are able to not only register the geometry of the vault in great detail, but also to measure the deflection of the structure under its self-weight non-intrusively and with good accuracy. Structural analysis of the vault has been carried out employing two approaches: a) by using simple geometric models of the vault and b) by using the detailed laser scanning data. Major differences between the two approaches are obtained in terms calculated deflection, highlighting the importance of detailed geometric survey for the analysis of historic structures. Detailed geometric survey data is shown to be critical in achieving accurate analysis results in structures whose deformation behaviour is mainly governed by their geometry.