Best Practice to Change Secondary Assignments to End Status

Oracle HRMS (Canada) - Version 12.1

Is there a best practice or recommendation when to change no longer used/terminated assignments to "End" status? What risks can be encountered when updating assignment status from "Terminated" to "End"? We have whole bunch of terminated secondary assignments that we want to clean up so they are not picked up in the payroll runs as this is causing issues when need to retry a pay run for a current primary assignments but have to delete the runs on the terminated assignments first due to assignment action interlock rule failure that prevents to re-run the process if there have been subsequent