1) The recieved bundle containing the export of the customers organizations does not know anything on id´s of a resource on the fhir server

You can check in FHIR Http - FHIR v5.0.0 (hl7.org) for Conditional Reference, you can reference to another resource using a search parameter, such as identifier.


2) Logic to implement to make sure that "head" organization resources are inserted and correctly linked to "child" organizations would be quite complex.

Using the previous method, you can be confident that, even if the child does not exist and the head exists they will be linked because of the conditional reference. It is needed to implement some strategies for incoming "child" that reference an Organization that is not present in the server.