Dynamic production and logistics systems along supply chains have to operate smoothly with each other in order to satisfy customer demand in time. This task becomes even more challenging in the presence of perturbations affecting the systems. In order to address this challenge, information concerning capabilities and employment level should be appropriately exchanged between production and transportation systems. Nevertheless different stakeholders perform the planning and control of the individual systems, making locally bounded decisions. In this article we present a new approach for the alignment of production and transportation processes that enables an advanced handling of perturbations on the operational level. To this end we introduce a trigger that indicates when a re-planning of existing schedules becomes necessary. We also present a collaborative planning approach that allows for an advanced management of perturbations and a dynamic vehicle routing concept for the on time ...