Republishing an MXD after adding layers to it or re-ordering them, used to mess up popups. That was supposed to be fixed in 10.3+. We upgraded to 10.5.1. Well, the layer IDs don't change, but it still messes up popups.
My idea is simple: if a user republishes an MXD, don't corrupt the webmap. Layers that are there already, stay put and their popups continue working the same. Also, new layers get added. So in other words, what's there, stays the same, and keeps working. (And if a layer was deleted in the MXD of course it would be removed also in the webmap).
My viewers now use the enable popups for all layers WAB mod, but I have a lot of custom popups I used AGOL HTML in the popup for. Re-adding the custom HTML over and over is frustrating. I hoped 10.3 fixed it; it has not. Will this be a goal for Esri - AGOL?