If there are new features added to the published service, they should come through. However, if you have defined popups and you've made schema changes (ie added, removed fields), these changes will not show up because the schema information is stored in the web map. Other people have asked for the ability to refresh the layer in the web map based on schema changes, but it's challenging to solve the problem, e.g., what should happen if you delete a field that is used in a popup. We'd have to define some interface that pointed out differences and allowed you to solve it--which is sort of recreating the popup. However, if you were to just add fields, some sort of refresh option to pick up the new fields would be useful. So, if this is what you are seeing, we are aware of the issue, but have no immediate solution.
Thanks,
Mike