The deformation of compliant parts during material handling is a critical issue that can significantly affect the productivity and the parts' dimensional quality. There are multiple relevant aspects to consider when designing end-effectors to handle compliant parts, e.g. motion planning, holding force, part deformations, collisions, etc. This paper focuses on multi-robot material handling systems where the end-effector designs influence the coordination of the robots to prevent that these collide in the shared workspace. A multi-disciplinary methodology for end-effector design optimisation and multi-robot motion planning for material handling of compliant parts is proposed. The novelty is the co-adaptive optimisation of the end-effectors' structure with the robot motion planning to obtain the highest productivity and to avoid excessive part deformations. Based on FEA, the dynamic deformations of the parts are modelled in order to consider these during the collision avoidance between the handled parts and obstacles. The proposed methodology is evaluated for a case study that considers the multi-robot material handling of sheet metal parts in a multi-stage tandem press line. The results show that a substantial improvement in productivity can be achieved (up to 1.9%). These also demonstrate the need and contribution of the proposed methodology.