FlexRay [9] is an automotive standard for high-speed and reliable communication that is being widely deployed for next generation cars. The protocol has powerful errordetection mechanisms, but its error-management scheme forces a corrupted frame to be dropped without any notification to the transmitter. In this paper, we analyze the feasibility of and propose an optimization approach for an application-level acknowledgement and retransmission scheme for which transmission time is allocated on top of an existing schedule. We formulate the problem as a Mixed Integer Linear Program. The optimization is comprised of two stages. The first stage optimizes a fault tolerance metric; the second improves scheduling by minimizing the latencies of the acknowledgement and retransmission messages. We demonstrate the effectiveness of our approach on a case study based on an experimental vehicle designed at General Motors.