The family of rare-earth tritellurides RTe$_3$ features charge-density-wave (CDW) order related to strongly momentum-dependent electron-phonon coupling. Similar to other CDW compounds, superconductivity is observed when the CDW order is suppressed via hydrostatic pressure [1]. What sets the heavier members of the RTe3 series apart is the observation of a second CDW transition at lower temperatures having an in-plane ordering wavevector $q_{CDW,2}\parallel [100]$ of almost the same magnitude but orthogonal to the ordering wavevector $q_{CDW,1}\parallel [001]$ observed at higher temperatures [2]. Here, we report an inelastic x-ray scattering investigation of the lattice dynamics of DyTe$_3$. In particular, we show that there are several phonon modes along both in-plane directions, which respond to the onset of the CDW transition at $T_{CDW,1}=308\,\rm{K}$. Surprisingly, these soft modes close to $q_{CDW,2}=(0.68,0,0)$ show strong softening near $T_{CDW,1}$ but do not exhibit any response to the lower-temperature transition at $T_{CDW,2}=68\,\rm{K}$. Our results indicate that the low-temperature CDW order is not just the 90{\deg} rotated analogue of the one appearing at high temperatures.