Using the CLASH-VLT survey, we assembled an unprecedented sample of 1234 spectroscopically confirmed members in Abell~S1063, finding a dynamically complex structure at z_cl=0.3457 with a velocity dispersion sigma_v=1380 -32 +26 km s^-1. We investigate cluster environmental and dynamical effects by analysing the projected phase-space diagram and the orbits as a function of galaxy spectral properties. We classify cluster galaxies according to the presence and strength of the [OII] emission line, the strength of the H$delta$ absorption line, and colours. We investigate the relationship between the spectral classes of galaxies and their position in the projected phase-space diagram. We analyse separately red and blue galaxy orbits. By correlating the observed positions and velocities with the projected phase-space constructed from simulations, we constrain the accretion redshift of galaxies with different spectral types. Passive galaxies are mainly located in the virialised region, while emission-line galaxies are outside r_200, and are accreted later into the cluster. Emission-lines and post-starbursts show an asymmetric distribution in projected phase-space within r_200, with the first being prominent at Delta_v/sigma <~-1.5$, and the second at Delta_v/ sigma >~ 1.5, suggesting that backsplash galaxies lie at large positive velocities. We find that low-mass passive galaxies are accreted in the cluster before the high-mass ones. This suggests that we observe as passives only the low-mass galaxies accreted early in the cluster as blue galaxies, that had the time to quench their star formation. We also find that red galaxies move on more radial orbits than blue galaxies. This can be explained if infalling galaxies can remain blue moving on tangential orbits.
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