Enterprises are demanded to collaborate and establish partnerships to reach global business and markets. However, due to the different sources of models and semantics, organizations are experiencing difficulties exchanging vital information electronically and seamlessly, even when they operate in related business environments. This situation is even worst in the advent of the evolution of the enterprise systems and applications, whose dynamics result in increasing the interoperability problem due to the continuous need for model adjustments and semantics harmonization. To contribute for a long term stable interoperable enterprise operating environment, the authors propose the integration of traceability functionalities in information systems as a way to support such sustainability. Either data, semantic, and structural mappings between partner enterprises in the complex network should be modelled as tuples and stored in a knowledge base for communication support with reasoning capabilities, thus allowing to trace, monitor and support the stability maintenance of a system’s interoperable state.