To maintain full autonomy, autonomous robotic systems must have the ability to self-repair. Self-repairing via compensatory mechanisms appears in nature: for example, some fish can lose even 76% of their propulsive surface without loss of thrust by altering stroke mechanics. However, direct transference of these alterations from an organism to a robotic flapping propulsor may not be optimal due to irrelevant evolutionary pressures. We instead seek to determine what alterations to stroke mechanics are optimal for a damaged robotic system via artificial evolution. To determine whether natural and machine-learned optima differ, we employ a cyber-physical system using a Covariance Matrix Adaptation Evolutionary Strategy to seek the most efficient trajectory for a given force. We implement an online optimization with hardware-in-the-loop, performing experimental function evaluations with an actuated flexible flat plate. To recoup thrust production following partial amputation, the most efficient learned strategy was to increase amplitude, increase frequency, increase the amplitude of angle of attack, and phase shift the angle of attack by approximately 110 degrees. In fish, only an amplitude increase is reported by majority in the literature. To recoup side-force production, a more challenging optimization landscape is encountered. Nesting of optimal angle of attack traces is found in the resultant-based reference frame, but no clear trend in amplitude or frequency are exhibited -- in contrast to the increase in frequency reported in insect literature. These results suggest that how mechanical flapping propulsors most efficiently adjust to damage of a flapping propulsor may not align with natural swimmers and flyers.