you can just create a new EmailMessage record in flow, with Case Id as relatedToId in EmailMessage record. Most of the data you need for EmailMessage should be available in the flow. You just need to map it to EmailMessage record. You can reference this https://developer.salesforce.com/docs/atlas.en-us.object_reference.meta/object_reference/sforce_api_objects_emailmessage.htm for the rest of the fields