Maybe this is just a fact of life, but I hope not. When I add layers to map services - by adding the layer to the authoting-mxd and overwriting an existing service, all the popups below the layer get messed up. I usually have to reload the service into a web map and reconfigure all the popups, which is extremely time-consuming.
Is there any way around this or is this "as designed?"
Another thing that happens, even when I have not added any layers, is that the attributes in the popup window are empty - they don't display values for fields that should have them - they are all blank.
Reloading the map service and (re) configuring popups is only solution.