The Flying-V aircraft could revolutionize commercial aviation, boasting a potential 25% increase in aerodynamic efficiency. Due to inherent design limitations regarding static stability, the need for a proper Flight Control System (FCS) is essential for the development of the aircraft. The concept of Hybrid Incremental Nonlinear Dynamic Inversion (INDI) was introduced to mitigate the insufficient stability margin encountered in existing sensor-based INDI systems due to sensor time delays, to achieve Level 1 Handling Qualities (HQ). Furthermore, the research introduces an exponential potential function-based command limiting Flight Envelope Protection (FEP) to enhance safety compared to the currently implemented linear-based FEP. The study compares and evaluates the effectiveness of the updated system under various flight conditions and parametric uncertainties. Results show improved stability margins and a safer FEP. However, additional research is required into actuator saturation and control allocation issues during the approach condition and to enhance fault tolerance.