In this paper we describe a novel strategy to reveal and handle complex dependencies in an incremental and distributed design processes even under the ubiquitous presence of uncertainties concerning model and design. We demonstrate in a case study how to handle epistemic design uncertainty in an iterative process and present how it is possible to selectively exclude dependency paths under certain concerns such as timing by including third party analysis results based on the used models into the dependency analysis. Since the implementation of our approach relies on modern graph analysis libraries it can scale to realistic problem instances.