Okay. This is a bit confusing with what you have, and what you want to do.
How do you want the updated hosted feature layer to be reflected in the Web Application, if you are not using that layer in the "customized" webmap.
Also please add a few snapshots to help us understand the scenario.
**Edit: If you have used Hosted Feature Layer Views in the custom web maps, the symbology of the views should also be changed (Item Details Page of the View > Visualization Tab).
Think Location