Modern concepts of supply chain and logistics development are changing dynamically, focusing not only on cost-reduction efficiency, but also a reorientation towards safety and fault tolerance, which leads to an increase in time and often the amount of logistics costs. Therefore, the problem of transformation of supply chains (SC) according to the criterion of fault tolerance involves the use of a life cycle architecture, which is an urgent problem of restructuring the entire system of commodity movement and complex objects—supply chains. The aim of the work is to change approaches and meanings to the interpretation of the principles of fault tolerance consideration based on the methodology of proactive management of the architecture of the supply chain lifecycle. This study is based on risk-based and system engineering methods that interpret the supply chain as a complex socio-techno-ecological system (“living organization”) that is able to constantly adapt to external conditions due to the ability to anticipate developments in conditions of high uncertainty, integration of various elements of the system to interact within a single architecture and life cycle processes. Architecture, as a key element of a closed-loop SC, represents a new class of system elements in the field of fault tolerance, assessment and management of systemic risks throughout the organization, as a single integral organism in automation conditions. The basic result of the research discussed in the chapter is not so much the expansion of the scale and volume of processed digital data, but the transition to flexible self-organization based on integrated predictive models with variable architecture and transparency of processes that expand the possibilities of supply chain management, taking into account sustainability and flexibility. The integrated architectural approach to the life cycle ensures coordinated and rapid interaction of processes and supply chain facilities based on the formation of a single trust-based information environment, the possibility of forecasting a tunable architecture and expanding the scope of application of digital twin’s technology.