I think there should be a tool to update field aliases. This generally is not a problem but, when I publish a service to ArcGIS Server and use the query/find/identify tasks and attempt to display the aliases, it is only displaying them from my MXD, not the stored aliases. And my users are getting frustrated. I think this would be a pretty easy thing to build. For now, I am going to have to waste my time building a tool to do this.
There could also be an option when publishing the service, to either use the mxd aliases or use the Geodatabase Aliases.