Frequency encoded photonic qubits promise a scalable path towards high-dimensional quantum information processing, but require efficient components for coherently mixing frequency modes. Coupled cavity modulators provide this functionality by using only a single driving microwave tone to couple hybridized optical supermodes. Here, we demonstrate a heterogeneously integrated thin-film lithium-niobate-on-silicon coupled-cavity modulator that realizes tunable bidirectional frequency mode transformations, including 50/50 beam splitting and near complete frequency swapping with >20 dB pump extinction at a 10 GHz supermode splitting. Because the electro-optic film is bonded onto a foundry fabricated silicon photonics platform, the approach is compatible with co-integration of photon pair sources, spectral filters, active tuning elements, and single photon detectors. We also bond thin-film lithium tantalate onto the same coupled-cavity platform, demonstrating material flexibility for scalable integrated frequency bin quantum photonic circuits.