Hi Nutan If you are using Current Structure for position assignment and payslip generation I would rather suggest you to use same structure Reassign organizational units and position so that it will not have an impact on payroll.
Firstly you need to identify How many organizational units and positions have to be changed ?
Organizational Structure is used mainly for Reporting You need to check Reporting Structure of Positions as well.
Check the data for single employee Execute payslip and post so that you will come where it is implicating Incase if there is change in cost centers.