My personal recommendation for when a patient is being seen basically for 2 separate visits (one NF or WC and another for regular health insurance) is to have 2 separate notes.
If records are needed by any carrier, they should be sent ONLY the relevant record. So NF should not be billed nor sent records containing flu shot information. And commercial carrier being billed for cold & flu shot services should not be billed nor sent records containing automobile injury information.
Each service and record should be appropriately coded and leveled based on that specific portion of the service. If it is one note, it is much more difficult to ascertain whether a prescription, or a test order was due to a particular visit.