It will be useful to know which ETL you are using, however it is important to consider when you transfer data. If you are creating a new record, specifying the owner is enough to set the field with EntityReference
Entity contact = new Entity("contact");
contact["firstname"] = "John";
Guid ownerId = new Guid("BFC777ED-5E79-E111-8489-00166D63156F");
contact["ownerid"] = new EntityReference("systemuser", ownerId);
service.Create(contact);
If you are updating a contact, you need to use AssignRequest as described in another section
Guid contactId = new Guid("90F8889F-EB95-E781-8417-000C44420CBC");
Guid newOwnerId = new Guid("BFCAA4ED-5E79-E781-8349-00155BB3156F");
AssignRequest assignRequest = new AssignRequest
{
Assignee = new EntityReference("systemuser", newOwnerId),
Target = new EntityReference("contact", contactId)
};
service.Execute(assignRequest);
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