Source-filter models are widely used in numerous audio processing fields, from speech processing to percussive/contact sound synthesis. The design of filters for these models—be it from scratch or from spectral analysis—usually involves tuning frequency and damping parameters and/or providing an all-pole model of the resonant part of the filter. In this context, and for the modelling of percussive (non-sustained) sounds, a source signal can be estimated from a filtered sound through a time-domain deconvolution process. The result can be plagued with artifacts when resonances exhibit very low bandwidth and lie very close in frequency. We propose in this paper a method that noticeably reduces the artifacts of the deconvolution process through an inter-resonance phase synchronization. Results show that the proposed method is able to design filters inducing fewer artifacts at the expense of a higher dynamic range.