This study investigates and optimizes chromatographic separation in a Centrifugal Partition Chromatograph. Therefore, a model system is separated in a single-disc rotor. The occurring loss of the stationary phase lowers the separation efficiency over time. We introduced a new mode of operation, called the redosing of the stationary phase, to counteract this hydrodynamic phenomenon. Experiments with redosing at an optimized operating point demonstrate almost constant separation performance over 12 h, reducing solvent consumption by 45% and increasing chromatographic resolution by 37%. The improvement in retention by 69% contributes to this enhancement. Accordingly, reference experiments without redosing were conducted as a benchmark, highlighting the automated mode’s benefits, as mentioned.