Multi-Level Hybrid Flying Capacitor (MLHFC) converters are emerging high energy density dc-dc converters. This paper presents an online feedback stability region detection and flying capacitor (FC) balancing technique for MLHFC converters. The feedback region detector monitors the FC voltage and the internal control signal of the FC control loop to detect the feedback region and adapt the controller accordingly. The proposed detector is control type independent and can be embedded e.g. in a digital Sliding Mode Controller (SMC). In this work, the feedback detection mechanism directly acts inside the controller to balance the FC voltage. The analyzed controller offers a wide range of possible applications, resulting in a very versatile controller for MLHFC converters. Simulation results highlight the effectiveness and robustness of the proposed control architecture.