I am doing a lot of testing with ArcGIS Enterprise (v10.5.1), federating ArcGIS Server with Portal, and ArcGIS Pro for publishing. One specific task I have just tested is overwriting a service created by ArcGIS Pro, or to use the latest terminology, overwriting a Web Layer.
In ArcGIS Pro (v2.1.2), when I chose Overwrite Web Layer I was presented with a warning reading, "If you overwrite this web layer, any popups configured or changes made to the web layer after it was initially published will be lost. This may affect existing clients using the layer by changing layer order or available fields." I had previously added the Portal map layer item to a map and configured a popup. As it turned out, the popup was not affected following the Overwrite, but I was more than a bit worried.
That warning message is very disconcerting. Why is this warning given, and under what circumstances will popups or other configurations be lost? Not knowing when configurations may be lost is not a good place to be.