Automatically reconfigurable fixtures allow adaptation to geometry changes during manufacturing by repositioning contact elements or adjusting contact forces. Flexible suction cup grippers are widely used as contact elements because they adapt to curved surfaces of flexible workpieces. During gripping, the bellows and the sealing lip exert an unwanted force on the workpiece. This causes a deformation of low stiffness workpieces and affects the machining accuracy during fixture reconfiguration. This paper presents a simulation model and an algorithm to counteract the workpiece deformation in automatically reconfigurable fixtures caused by nonlinear stiffness of vacuum grippers during positioning through control of the vacuum.