Revenue have just issued an eBrief today which gives updated guidance and examples of how to recoup overpayments. The situations are described in the context of Smart PAYE also. Please see below from the revenue website and also corresponding link to the relevant documentation :
Recoupment of Overpayments of Salary by an Employer from an Employee
Tax and Duty Manual Part 42-04-70 – Recoupment of Overpayments of Salary by an Employer from an Employee – has been amended to provide updated examples for recoupment of ‘in-year’ and ‘out of year’ salary overpayments and to incorporate updates effective from 1 January 2019 concerning realtime PAYE data.