The active neutral-point-clamped (ANPC) topology enables the use of high–figure-of-merit (FoM) devices with voltage ratings below the system requirement, provided the neutral midpoint remains stable. Midpoint-voltage control loops can undergo polarity inversion—a reversal of loop gain—that may cause regulation failure. This paper presents a digital controller that detects polarity inversion in real time and reverses control polarity without prior knowledge of system parameters. The method is demonstrated on an SIadj{8}{kilowatt}, SI{300}{kilohertz}, GaN-based three-phase ANPC dual active bridge (DAB) converter for 400-to-800~V electric vehicle charging. Experimental results show stable regulation over a wide load range, recovery after inversion, and continuous balancing during transients, confirming suitability for high-performance SIadj{800}{volt} ANPC architectures.