A unique opportunity to investigate the sensitivity of modal parameters of complex vaulted masonry systems to geometric distortions due to abrupt changes in boundary conditions is found in Beverley Minster, UK. Over the last eight centuries, the accumulated support settlements of the buttresses have pulled the main nave walls outwards, causing severe Sabouret cracks along the edges of masonry vaults. At certain locations, the separation of the walls from the nave vaults has reached 150 mm, while bays closer to the main crossing tower remain integral with the walls. Due to large deformations, the crown of the damaged vaults sags approximately 200 mm relative to the undamaged vaults. The sag of the crown and inverse curvature of the damaged vaults are visually observable. To compare different states of the vaulted system, representative sections of both undamaged and damaged vaults were subjected to modal analyses by measurable hammer impact excitation. The deviations of the natural frequencies and mode shapes between the two cases are quantified. The discrepancies of the modal parameters are found to be as low as the measurement errors, and thus insufficient to yield conclusions on the state of damage to the vaults. However, magnitudes of frequency response functions are significantly greater for the damaged vaults.