Nanosecond pulsed laser melting can be used to rapidly recrystallize ion-implanted Si through liquid phase epitaxy. The rapid resolidification that follows the melting results in a supersaturation of impurities and hyperdopes the Si, inducing novel optoelectronic properties with a wide range of applications. In this work, structural changes in the Si lattice in Au-hyperdoped Si are studied in detail. Specifically, we show that the local skewing of the lattice observed previously in regions of extremely high Au concentrations (>1.4 at. %) can be related to the displacement of Au from perfect lattice positions. Surprisingly, although the incorporation of the larger Au atoms into Si is expected to cause swelling of the lattice, reciprocal space mapping shows that a small amount (0.3 at. %) of lattice contraction (decrease in lattice parameter) is present in the hyperdoped layer. Furthermore, positron annihilation spectroscopy shows an elevated concentration of vacancies in the hyperdoped layer. Based on these observations and with the aid of density functional theory, we propose a phenomenological model in which vacancies are kinetically trapped into lattice sites around substitutional Au atoms during resolidification. This vacancy trapping process is hypothesized to occur as a means to minimize lattice strain and may be universal in pulsed laser melted Si systems.