The problem of updating the logic of ITS operation when introducing innovative functions and adapting to the requirements of a particular educational institution (localization) is considered. Arguments in favor of multi-stage decision-making based on the model of P.K. Anokhin are given. The architectural solution of such ITS is proposed and the stages of generalization of processed data from the digital educational footprint are described. The possibilities of using the mechanism of recommender systems and fuzzy logic for reconfiguring the logic of decision-making are discussed. By the example of using the mechanism of competency development assessment and course individualization, the process of changing the logic to fit the new functionality of the system is shown. The results of implementation in the ITS are demonstrated for an experimental ITS used in the educational process of the master’s degree program at the Siberian Federal University.