Nonthermal plasma flow tube reactors are industrially scalable systems for the production of nanocrystal (NC) based materials and coatings. One key advantage of nonthermal plasma synthesis is the ability to both synthesize NCs and deposit films in a single reactor, as at the reactor outlet, NCs can be inertially deposited onto a target substrate. The size and morphology of deposited particles can substantially influence the film structure and function. Though NCs are typically near-spherical and monodispersed as-produced in plasma synthesis reactors, NC charge and growth dynamics can be altered substantially when NCs are sampled out of the plasma and through the spatial afterglow region, affecting deposition. Experiments have demonstrated changes of NC size and charge in the spatial afterglow; however, these dynamics remain unexplored and unexplained via theory and simulation. To address this, we developed a constant number Monte Carlo (CNMC) simulation model to examine the mechanisms of NC decharging and growth in the spatial afterglow of plasma flow tube reactors. Collisions between NC and plasma species, diffusive deposition, and electron desorption from NCs are incorporated in the CNMC simulation. The simulation results are specifically compared with previous experiments on Si NCs synthesized from a low pressure Ar-SiH4 nonthermal plasma reactor. The experiment-model comparison shows that CNMC models can be implemented which accurately model NC size distribution evolution in a spatial afterglow. Simultaneously, results show that improved collision models, energetic species diffusion models, and electron desorption models will be necessary to accurately depict NC dynamics in spatial afterglows.