Hi Stephen

Can you check the following element settings

• Source contains all records - check if this is set to Yes if it is then missing records from the file will be deleted
• Check if the Allowed HR Import actions has Delete unticked if no records are required to be deleted
• Check the empty string behaviour - empty strings erases existing data

Were the job assignments created with the HR Import - this is required so they are updatable with the HR Import . 

regards