In Flow Graph, you can communicate directly to and from a prefab instance just like an entity by using prefab events. Just create an event inside a prefab, give it a name and then reference the prefab instance as you normally do an entity.
Steps to use prefab events
Inside any prefab flowgraph, add Prefab:EventSource nodes for each event you want (note: you must be inside a prefab's flowgraph otherwise will get errors)
Assign a name to the event
Outside the prefab's flowgraph, in any entity's flowgraph, select a prefab instance you want to send/receive events from and click "Add Selected Entity":
Connect logic to the prefab instance events
Important notes
Whenever deleting Prefab:EventSource nodes, this will remove the event but won't remove flownode port connections to that event. As a rule of thumb, always remove all uses of that event before removing.
Always make sure to communicate with other level designers when removing prefab events as you might have removed the event which is referenced in other levels.