Soft amphoteric microgel systems exhibit a rich phase behavior. Crystalline phases of these material systems are of interest because they exhibit photonic stop-gaps, giving rise to iridescent color. Such microgel systems are promising for applications in soft, switchable, and programmable photonic filters and devices. We here report a composite microgel system consisting of a hard and fluorescently labeled core and a soft, amphoteric microgel shell. At pH above the isoelectric point (IEP), these colloids easily crystallize into three-dimensional colloidal assemblies. By adding a cyclic lactone to the system, the temporal pH profile can be controlled, and the microgels can be programmed to melt, while they lose charge. When the microgels gain the opposite charge, they recrystallize into assemblies of even higher order. We provide a model system to study the dynamic phase behavior of soft particles and their switchable and programmable photonic effects.