This issue is not reproducible in ArcGIS Online as the provided service is not a Sample Service 6 feature service. If the issue occurs, contact Esri Support Services as additional information is required for further investigation.
Publish published a service that originally had a domain with two coded values on a field called Enabled, and the layer symbolizes on that field.
Go into the Data tab and add two more values to the list, then into the Visualization tab to make sure those two new values show up on the symbology field, and save the Visualization.
Now when opening the layer in the map viewer, all 4 values under the legend.