Unlike a SQL Server service instance for example, you will not need to manually refresh a SharePoint 2013/Online service instance. Typically, adding/removing/changing a SharePoint list/library will trigger the SmartObject/view/form regenerate option:
https://help.nintex.com/en-US/nintexautomation/userguide/current/Content/Create/K2ForSharePoint/Change-SP-List-Library-Structure.htm
Where you should take the applicable action. If you need to force a list/library to regenerate, you can try adding a “test” single line of text column for example, regenerating, then remove this column and regenerating again.
A Service Instance of the SharePoint service is created and configured automatically when installing the K2 for SharePoint App on a SharePoint site collection. Additional Service Instances will be created for each new site collection that is integrated with the product
You cannot manually register, refresh, modify or delete service instances for the SharePoint service types (unless directed by Nintex Customer Central to do so). You must use the K2 for SharePoint App registration wizard to create and manage Service Instances.
https://help.nintex.com/en-US/nintexautomation/userguide/current/Content/ServiceBrokers/SharePoint/SharePoint.htm