Data published to ArcGIS Online can be updated using the Overwrite Entire Layer and Append Data to Layer options. However in some cases, the Overwrite Entire Layer option is not available when:
Data is published from ArcGIS Desktop
When data is originally published from ArcGIS Desktop, the Overwrite Entire Layer option is not available on the item details page. A Service Definition is created during the publishing process to ArcGIS Online. To overwrite the published service, the Service Definition must be present. If the Service Definition is deleted by accident or not uploaded to ArcGIS Online, the service cannot be overwritten from ArcMap when publishing, but can be overwritten from ArcGIS Pro. Refer to ArcGIS Online: Create hosted feature layer views for more information.
Data is published directly by uploading to ArcGIS Online
The hosted service published directly to ArcGIS Online can be overwritten from the item details page and ArcGIS Pro.
However, if the source item is deleted, the Overwrite Entire Layer option is not available on the item details page. If a layer from the hosted feature layer is a part of a join where the result is a hosted feature layer view, the Overwrite Entire Layer option is not available on the item details page, and overwriting from Desktop fails. If the join results are saved as a hosted feature layer, it does not affect the overwrite capability.