Layer order after map service updates

Question

We have published maps in our ArcGIS Online subscription that contain map services from our ArcGIS for Server v10.1.  We have configured attribute pop-ups for map service layers in the online published map.  When we add, remove or rearrange data layers in the table-of-contents of our map service source MXD and then refresh that map services on our server, the attribute pop-ups in the online map are all messed up.  It's as if the REST layer order is fixed in the online map and if layers are later added, removed or rearranged in the source service, the online map can't keep track of the refreshed REST layer order.  Is this what's happening?

AbdulJabbar1 · Answer

After you finish everything with your MXD, try republishing your service. Hope the things will resolve for you.