We have a few basemaps that have a reference layer (Navigation Overlay) of highway shields, route names, etc.
While configuring the App, this layer is visible and working how we expect (same is true for the 'map' - works fine there as well), however, once the App is saved and viewed, the reference layers no longer exist.
? Where do they go?
*everything is shared publicly.
No, in an AGO map you can add a reference layer and then "move it to the basemap". The first image kind of illustrates this. The "Navigation Overlay" has already been moved to the basemap. That is the layer that is disappearing in a published WAB.