Hi Yug,
It's because of your payroll control record.
1. Go thru PA03 and delete your control record.
2. Create one for a date before you would apply changes, for example one month before.
3. Apply your changes.
4. Delete current payroll control record in PA03 again
5. Create your original control record in PA03 (What you had in step 1).
Cheers,
Omid