We have an employee who has not worked all year, but remains an employee of a client. Anyone know what is the best way to do her STP Finalisation?

You can proceed with your client's payroll as normal. If the employee has zero earnings reported to the Australian Tax Office, she won't appear in the Single Touch Payroll wizard and requires no finalisation action. You can leave her profile as is until her next pay run, or mark her as inactive if she isn't returning. 

You can read through this guide for more details: Single Touch Payroll (STP) guide.

Please don't hesitate to reply if you have other questions or concerns.