The process of republishing or updating an existing Map Service is cumbersome for complex ArcGIS Online maps. One item is that after republishing the map service and getting it online, all of the pop up window customization and layer on/off status is lost, and you have to remember all that then recreate it in order to maintain a consistent map product. When you have multiple map services in an online map, and multiple layers in each service, this gets pretty tedious for maps that get routinely updated.
Our current workaround is to maintain a separate document that details all of the customization settings for the individual layers, then redo all the customization after re-publishing the map services. That is a lot of redundant work every time a map gets updated.