Hi Nikhil,
There are many options to choose from.
(a) As stated above, you can use transaction FPPNR to upload the rejected transactions into SAP, if you are receiving the rejected file from the bank in ACH format.
(b) You can also use transaction FPB5 for processing the rejected payments that you get from the file.
(c) If you are receiving the rejected payments from the bank through an account statement,you can also use FPB7/FPB17 for processing them in SAP.
Hope it helps...
Thanks,
Amlan