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The Laser Interferometer Space Antenna (LISA) is a European Space Agency mission that aims to measure gravitational waves in the millihertz range. The three-spacecraft constellation forms a nearly-equilateral triangle, which experiences flexing along its orbit around the Sun. These time-varying and unequal armlengths require to process measurements with time-delay interferometry (TDI) to synthesize virtual equal-arm interferometers, and reduce the otherwise overwhelming laser frequency noise. Algorithms compatible with such TDI combinations have recently been proposed in order to suppress the phase fluctuations of the onboard ultra-stable oscillators (USO) used as reference clocks. In this paper, we propose a new method to cancel USO noise in TDI combinations. This method has comparable performance to existing algorithms, but is more general as it can be applied to most TDI combinations found in the literature. We compute analytical expressions for the residual clock noise before and after correction, accounting for the effect of time-varying beatnote frequencies, previously neglected. We present results of numerical simulations that are in agreement with our models, and show that clock noise can be suppressed below required levels. The suppression algorithm introduces a new modulation noise, for which we propose a partial mitigation. This modulation noise remains the limiting effect for clock-noise suppression, setting strict timing requirements on the sideband generation.