The present application discloses systems and methods for operating a stimulation prosthesis that contains a command module and a stimulator module that communicate by a data link. The stimulation prosthesis has at least two operating states: a configuration state and a stimulation state. In one embodiment, the stimulation prosthesis may use a communication protocol that is suitable for the current operating state. The risk of unintended transitions between the operating states due to data transmission errors is substantially eliminated. And in accordance with another embodiment, in addition to switching stimulation strategies, the stimulation prosthesis may also switch stimulation data formats to a format that is optimized for the new stimulation strategy.
