We have studied processes of interaction of pulsed laser radiation with resonant groups of plasmonic nanoparticles (resonant domains) in large colloidal nanoparticle aggregates having different interparticle gaps and particle size distributions. These processes are responsible for the origin of nonlinear optical effects and photochromic reactions in multiparticle aggregates. To describe photo-induced transformations in resonant domains and alterations in their absorption spectra remaining after the pulse action, we introduce the factor of spectral photomodification. Based on calculation of changes in thermodynamic, mechanical, and optical characteristics of the domains, the histograms of the spectrum photomodification factor have been obtained for various interparticle gaps, an average particle size, and the degree of polydispersity. Variations in spectra have been analyzed depending on the intensity of laser radiation and various combinations of size characteristics of domains. The obtained results can be used to predict manifestation of photochromic effects in composite materials containing different plasmonic nanoparticle aggregates in pulsed laser fields.