This study offers a comprehensive scientific and methodological apparatus for capitalizing knowledge in the field of innovative technologies for chemical and biological safety. Through the prism of the analysis of semantic flows of patent and publication landscapes, as well as the development of mathematical models of the mutual influence of endogenous and exogenous determinants, the work focuses on the optimization of research projects and knowledge engineering for actors in interdisciplinary scientific and technical programs. The results include methodologies for assessing the influence of business environment factors, defining innovation strategies, analyzing R & D performance, and managing the risks of scientific human capital migration, adapted to the conditions of global transformation and sanctions pressure.