Hi Sandeep,
This is not the correct that all amount would be goes to new cost center due to retro effect.
So for that as per cost center wise amount will be balancing. Since employee was in that cost center and had received more amount and due to retro recovery goes to that cost center itself.
If you want to post in new cost center then has to stop the retro for them and give the addition or recovery amount has to upload in IT14 & IT15. Then it will post to current cost center.
Regards,
Sankarsan