If there are changes in the services being consumed from a SOAP web service or if you want to modify the list of consumed methods, you just need to refresh it in Service Studio.
For that, do the following:
In the Logic tab, open the Integrations folder;
Under the SOAP element, right-click the SOAP Web Service you want to refresh and select Refresh SOAP Web Service;
The Refresh operation will re-read the WSDL for the service and show you the list of available methods, allowing you to remove/add any consumed methods.
Change the list of consumed methods by checking or unchecking them, and press "Finish" to apply your changes.
If a consumed method is no longer present in the service definition it will be shown as "(outdated)", while new methods in the service definition will be shown as "(new)".