Exhaust Gas Recirculation (EGR) was recently introduced in large marine two-stroke diesel engines to reduce NOx-emissions. Controlling EGR flow during accelerations, while keeping good acceleration performance is challenging, due to delays in the scavenge receiver oxygen measurement and upper limits on fuel for avoiding black smoke. Previous oxygen feedback controllers struggled during accelerations, but a new EGR-controller based on adaptive feedforward (AFF) has been successful. Nevertheless, further analysis and tests are required before deploying the controller to more EGR ships. A simulation platform is a great asset to test controllers before expensive real-world experiments are conducted. A new EGR flow controller is proposed and tested in a complete ship simulation model. Several acceleration scenarios show that the low load area is most challenging. Controller robustness is analysed in this area, showing that pressure sensor bias in the EGR flow estimator is the most critical factor, which could lead to black smoke formation. This can be prevented with sensor calibration or by using a differential pressure sensor. Errors in the parameters of the flow estimators are not as important. This is a useful result because the right parameters of the flow estimators might be difficult to obtain, on a new engine.