Methods and systems for fault mitigation in an engine system. For ordinary operation, a set of control signals are generated after calculating airflows within the engine system using a set of flow models linked to components of the engine system, while underweighting or omitting an output of a sensor in the engine system. When a fault is identified, the set of flow models is analyzed differently by underweighting or omitting one or more flow models in favor of using the sensor output. By so doing, the engine system can continue to be operated without triggering an on-board diagnostic alert requiring cessation of operation.