Hi,
Finally found solution through EK02.
Here is basic crux for derivation at the time of invoicing.
Profit center gets derived through Contract (through COKEY). If this value needs overriding then field NOCRCT (should be X) with proper values in COKEY at EK02 level.
Moreover, to ensure that it is working always go for full reversal (EA13) and then do rebilling and reinvoicing.
Hope it helps to others who may have to face such requirement from business.
Regards,
Paresh