In amorphous solids, a non-negligible part of thermal conductivity results from phonon scattering on the structural disorder. The conversion of acoustic energy into thermal energy is often measured by the dynamical dtructure factor (DSF) thanks to inelastic neutron or x-ray scattering. The DSF is used to quantify the dispersion relation of phonons, together with their damping. However, the connection of the dynamical structure factor with dynamical attenuation of wave packets in glasses is still a matter of debate. We focus here on the analysis of wave-packet propagation in numerical models of amorphous silicon. We show that the damped harmonic oscillator model fits of the dynamical structure factors give a good estimate of the wave packets mean free path, only below the Ioffe-Regel frequency. Above the Ioffe-Regel frequency and below the mobility edge, a pure diffusive regime without a definite mean free path is observed. The high-frequency mobility edge is characteristic of a transition to localized vibrations. Below the Ioffe-Regel frequency, a mixed regime is evidenced at intermediate frequencies, with a coexistence of propagative and diffusive wave fronts. The transition between these different regimes is analyzed in detail and reveals a complex dynamics for energy transport, thus raising the question of the correct modeling of thermal transport in amorphous materials.