I would reopen the claim, fix the problems associated with the unpaid CPT codes such as getting corrected diagnosis codes or adding the correct modifier and rebill the whole claim. It is my experience that insurance company claim software will mark the paid code a duplicate and reprocess the other codes for payment. If whatever caused the original codes to be denied is corrected and is a paid benefit, those codes will be paid seperately. If the error is in using the wrong CPT code, such as the incorrect age range on a preventive care exam, then I have indeed deleted the unpaid code and entered the correct CPT and ICD9 code and rebilled it. Again the payment software will not repay the previously paid codes.