We are just about to implement our new AGOL based mapping application and I keep running into this issue. We have a dedicated server running ArcGIS Server 10.3. The MXD document we are publishing resides there and this service gets loaded into AGOL as a map image layer. This map image layer is included in our web map. I spent a LOT of time configuring the attributes for each of the layers in this web map. After I was done we decided to add some more layers to the original MXD. We updated the map service on our server by overwriting it. The map image layer on AGOL shows all the new layers we added via the REST endpoint. When I reopen the web map it also shows all the new layers that were added (yea!), but when I go to click on a feature, the resulting popup window shows the attributes for the old layer that was originally in that spot within the Table of Content order (boo!). The only way I have found to fix this is to delete the entire image layer from my map, reimport it, and reconfigure all the attributes again (immense boo!).
So, it just seems that the AGOL web map isn't capable of reordering the layerIDs based on the new stuff that has gotten added in. Does anybody know a way to make it do this? I can't imagine that ESRI wouldn't allow for the addition of new data without having to reconfigure every single data layer in your web map.
Thanks in advance,