The distinct optical signatures of aligned single and double Au atom chain structures, grown on vicinal Si(111) substrates, have been identified using reflectance anisotropy spectroscopy (RAS). Deposition of 0.04 monolayers (ML) of amorphous Si (a-Si) at room temperature perturbs the anisotropic optical response of the double chain structure. By one third of a monolayer, no significant optical anisotropy associated with the chains remains. No anisotropic response re-emerges at higher coverages, up to 4.6 nm (14.5 ML) where there is recent evidence that the crystal structure of the double chain phase is maintained under the cap. The RAS results show that the anisotropic properties of the phase are quenched by a-Si adsorption, even though the crystal structure of the capped phase appears to be preserved.