Neutral point clamped inverters, such as NPC, ANPC, or T-Type inverters, have emerged as competitive solutions for specific automotive traction applications due to the increase in DC-link voltage levels up to 800 V. Besides improved harmonic performance, certain 3-level inverter structures can provide a reconfigured failure mode operation in case of a semiconductor failure by applying a permanent neutral point connection in the faulty phase leg. This feature is a vital factor in the design of traction inverters, particularly in the context of fault-tolerant autonomous vehicles. During failure mode operation, none of the neutral point balancing techniques found in current literature are practical. Addressing this issue is crucial since the neutral point stress is high in this mode of operation. Therefore, this paper investigates the impact of stationary and dynamic neutral point voltage deviations on the motor flux in electric machines and offers a compensatory strategy for these errors. Furthermore, a new neutral point control method is presented that balances stationary neutral point voltage deviations by using a phase angle dependent voltage shift in the α/β-plane. All proposed strategies are first discussed theoretically and then verified by simulation and measurements on an 800 V IPMSM machine test bench.