This paper introduces a dual-mode controller for multi-level flying capacitor boost converters that provides minimum possible voltage deviation, seamless mode transitions, and the flying capacitor size reduction. These advantages are obtained by modifying the switching sequence during transients. The modification eliminates a potential delay in the output capacitor charge recovery and, at the same time, decouples the flying capacitor, eliminating large current spikes through it. The operation of the controller is verified with a Vin in [1.5V, 5V] to Vout=10V, 250kHz, 30W experimental prototype.