Use a shadow entity to import the flat file to this entity. Then use microflows to transport the data from this shadow entity to all your main entities and set the references with these microflows. This way you can also validate your data before import to main entities.
[EDIT] Let's say you have a flat file with a customer and a order. After the import all this data goes to one entity. Now create a microflow that looks up the customer in your main entities. Then check if all your customer data is still valid or otherwise update the customer record with the data from the import.
Then try to find the imported order. If not found create a new order object, set the reference to the found customer and update the order record with the imported data.
Do not forget to make a fault log where you log all the import faults. This way you can track when the last import was and what errors occured during the import.