Hi Tim,
If you have 3 assignments being paid under one tax reference i.e. 12345, 12345-2, 12345-3, you should have the aggregated flag set. When you need to transfer the assignments across to the new payroll you will have to create them as a new employee with 3 new assignments. This is because if you were to end the original 3 assignments, create 3 new assignments, the payroll would cause the EOY to fail due to the PAYE aggregation being ticked and the Payrolls having different tax references.
Have fun
Paul