How to prevent zero hour/zero Salary assignments from pulling into Calculate Payroll flow

Summary:

Does anyone know of a way to prevent zero hour or zero salary assignments (not talking about time card, but the assignment) from pulling into the calculate payroll process? 

The problem is that departments don't tell HR sometimes weeks, months, even years later about the employees needing to be retro termed,and because they have been pulled into payrolls with zero pay/zero salary, we are unable to retro term them and have to use the end date of the most recent payroll and have the department add a comment about what the actual date should have been.

The quantity is too many to roll back every zero hour/zero pay . (5-10 employees per week on avg)