This paper discusses the development and implementation of the architecture of a Framework for Aerospace Vehicle Reasoning, 'FAVER'. Integrated Vehicle Health Management systems require a holistic view of the aircraft to isolate faults cascading between aircraft systems. FAVER is a system-agnostic framework developed to isolate such propagating faults by incorporating Digital Twins (DTs) and reasoning techniques. The flexibility of FAVER to work with different types and scales of DTs and diagnostics, and its ability to adapt and expand for previously unknown faults and new systems are demonstrated in this paper. The paper also shows the novel combination of relationship matrix and fault attributes database used to structure the knowledge of FAVER's expert system. The paper provides the working mechanism of FAVER's reasoning and its ability to isolate faults at the system level, identify their root causes, and predict the cascading effects at the vehicle level. Four aircraft systems are used for demonstration purposes: i) the Electrical Power System, ii) the Fuel System, iii) the Engine, and iv) the Environmental Control System, and the use case scenarios are adapted from real aircraft incidents. The paper also discusses the pros and cons of FAVER's reasoning via demonstrations and evaluates the performance of FAVER's reasoning through a comparative study with a supervised neural network model.