When you create a service using data wizard then there are 2 files that get generated under services.<service_name> pkg. If you want any method on client side only then add it in derived class else you need to add method in server php and click on refresh option in data/service wizard panel. You can see this new method in super class under the same package.
Are you seeing any messages/errors displayed by Flash Builder when you try to refresh. It will help us to reproduce this issue if you can share the PHP file and Flash Builder error log. You can find the Flash Builder error log here Help -> About Flash Builder - > Installation Details -> View Error Log.