The evolution of the polymer structure during nanocomposite formation and annealing of silica-latex nanocomposites is studied using contrast-variation small angle neutron scattering. The experimental system is made of silica nanoparticles (Rsi ≈ 8 nm) and a mixture of purpose-synthesized hydrogenated and deuterated nanolatex (Rlatex ≈ 12.5 nm). The progressive disappearance of the latex beads by chain interdiffusion and release in the nanocomposites is analyzed quantitatively with a model for the scattered intensity of hairy latex beads and an RPA description of the free chains. In silica-free matrices and nanocomposites of low silica content (7%v), the annealing procedure over weeks at up to Tg + 85 K results in a molecular dispersion of chains, the radius of gyration of which is reported. At higher silica content (20%v), chain interdiffusion seems to be slowed down on time-scales of weeks, reaching a molecular dispersion only at the strongest annealing. Chain radii of gyration are found to be unaffected by the presence of the silica filler.