The objects of the study are parallel-structure machine systems with redundancy associated with safety assurance of continuous material flow. The problem concerns systems in which the supply of materials takes place continuously (24 hours a day), and the system of operated machines must ensure the receipt and movement of the material at a strictly defined time and in the desired quantity. It is a system where the presence of a failure poses a threat to human life and environmental degradation. This paper presents a method for system condition assessment and upgrading for maintaining proper operation under conditions of continuous operation. A database of information about the current parameters of the system components (measurements, monitoring) is necessary for condition assessment. The method also uses lean techniques (including TPM). System evaluation and selection criteria for a suitable structure in terms of further operation were proposed. Exemplification was performed for an underground mine drainage system. As a part of the identification, selected parameters of the system components were measured, and their characteristics (motors, pumps, pipelines) were developed. The results of the analysis and the values of the adopted criteria were compared to the indicators for new pump sets. A two-option system upgrade was proposed, in addition to machine operating schedules, maintenance periods, and overhaul cycles.