The merge generated skeleton file option can be enabled in the web service preferences on the Resource Management page. This option is enabled by default. If it is enabled, when a skeleton file of the same name already exists in the workspace, the newly generated skeleton file will merge with the existing skeleton file. Enable this to preserve code that you have already modified in the existing skeleton files.
Note that when this preference is enabled, if you change the return type of an interface, the resulting skeleton file will have a method returning the type as defined in the new interface but would have a method body from the original skeleton file (which would be returning a different type). This will result in an compilation error that the you will have to correct manually.