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Abstract Kagomé metals are widely recognized, versatile platforms for exploring topological properties, unconventional electronic correlations, magnetic frustration, and superconductivity. In the RV6Sn6 family of materials (R = Sc, Y, Lu), ScV6Sn6 hosts an unusual charge density wave ground state as well as structural similarities with the AV3Sb5 system (A = K, Cs, Rb). In this work, we combine Raman scattering spectroscopy with first-principles lattice dynamics calculations to reveal phonon mixing processes in the charge density wave state of ScV6Sn6. In the low temperature phase, we find at least four new peaks in the vicinity of the V-containing totally symmetric mode near 240 cm−1 suggesting that the density wave acts to mix modes of P6/m m m and $$R\bar{3}m$$ R 3 ¯ m symmetry - a result that we quantify by projecting phonons of the high symmetry state onto those of the lower symmetry structure. We also test the stability of the short-range ordered density wave state under compression and propose that both physical and chemical pressure quench the effect. We discuss these findings in terms of symmetry and the structure-property trends that can be unraveled in this system.