Excess quasiparticles play a crucial role in superconducting quantum devices ranging from qubits to quantum sensors. In this work we analyze their dynamics for phase-biased finite-length weak links with several Andreev subgap states, where the coupling to a microwave resonator allows for parity state (even/odd) readout. Our theory shows that almost perfect dynamical polarization in a given parity sector is achievable by applying a microwave pulse matching a transition in the opposite parity sector. Our results qualitatively explain key features of recent experiments on hybrid semiconducting nanowire Josephson junctions and provide theoretical guidelines for efficiently controlling the parity state of Andreev qubits.