Currently you have to configure and save a separate web map for each app, if the map has different layers or filters applied.
Allow the user to create one web map containing all of the published layers, turned off.
In the App, such as Web App Builder or Dashboards, allow the user to turn on and filter the layers needed for the app. The app saves these settings.
This creates a cleaner publishing process. The user only has to maintain the published layers in one map, and the app remembers the layer settings. If the database schema gets updated, and the layers have to be republished, only one web map must be updated. The App settings remain the same.