Complex engineering systems include several subsystems that interact in a stochastic and multifaceted manner with multiple failure modes (FMs). The dynamic nature of FMs introduces uncertainties that negatively impact the reliability, risk, and maintenance of complex systems. Traditional approaches of adopting standalone techniques for managing FMs independently at various stages of the asset life cycle pose challenges related to utilisation, costs, availability, and in some cases, accidents. Therefore, this paper proposes a composite hybrid framework comprising four independent hybrid models for comprehensive through-life failure management and optimisation. The first hybrid model entails failure mode, effects, and criticality analysis (FMECA) and fault tree analysis (FTA) to identify critical FMs and overall subsystem failure rates. The second hybrid model analyses FMs caused by multiple subsystems using hybrid dynamic Bayesian discretisation. The third hybrid model adopts a hybrid Gaussian process regression machine learning technique to evaluate wear loss. The fourth hybrid model evaluates the overall risk using a Bayesian factorisation and elimination method based on multiple failure causes. Finally, a decision-making step is used to evaluate the results of the previous four steps to decide an appropriate maintenance strategy. The proposed method is verified through a case study of a UK-based train operator's pantograph system. The results show that the maintenance inspection intervals and strategy obtained using the proposed framework strike a good balance between safety and fleet availability.