Whenever you make manual changes to the configuration, you should replicate the changes back into the Administration server repository as follows:
Manually edit server instance's configuration files as you would do with the earlier version of Web Server (Not recommended).
Start the Administration Server.
For pulling the changes back to the Administration Server repository, execute the following command.
wadm> pull-config --user=admin --config=CONFIG_NAME
The operation may take some time depending on the configuration.
Always use the Administration Console or the wadm CLI to edit the settings. When you invoke pull-config only the contents of the <instance_dir>/config directory will be pulled into the configuration store from Sun Java System Web Server Update 1.