We've been working in a FHIR-compliant REST API with IBM IIB that allows interoperation between a Laboratory Information System (LIS) and a Hospital Information (HIS) System with EHR (Electronic Health Record), we hit a wall when we started thinking about resources that were not present on both systems HIS and LIS. This was our approach.
Our customer LIS (Laboratory Information System) resides in a different location than the HIS/EHR (Hospital Information System / Electronic Health Record), the master data on both systems is not shared. As a result, we need, very frequently, to post HL7 FHIR resources that we do not know if they exist in the remote system.
If we used contained/embedded resources, we would not have any control of what operation should be executed with the transferred resource. Using embedded resources for groups of data would mean exchanging information such as DiagnosticOrder with ALL required resources in a single transaction.
With bundles we can state an operation for every single resource (GET POST PUT DELETE) and re-use the resource in a future interaction, making it possible to fully handle every resource with individual REST operations.
If you want to learn more about our mobile healthcare interoperability, HL7 FHIR with IBM Integration Bus and IIB infrastructure, our team will be happy to discuss your specific requirements.