When adding a layer to a feature service and overwriting the service using ArcMap or ArcGIS Pro, the added layer is not displayed on the web map after republishing the feature service to ArcGIS Online. However, when accessing the REST endpoint of the feature service, the added layer is displayed.
This is expected behavior when overwriting a feature service in a web map. When a feature service is overwritten, the JSON file of the feature service is updated to reflect the changes. However, the JSON file of the web map containing the feature service remains static and thus, any changes made to the services are not reflected in the web map.
As a workaround, remove the existing feature service from the web map; add the new republished feature service containing the new layer, and save the web map. The added layer is displayed on the web map and in the Contents pane.
Note: When removing the existing feature service, the pop-up configurations of the feature service are not retained in the web map. The pop-ups must be configured again for the new feature service. For more information on configuring pop-ups, refer to Configure pop-ups.