Well, Im only assuming but perhaps a transfer of funds to another account gave an impression to the officer that the Transfer IN at the destination bank account is a receipt of funds of a significant amount without an explanation (as the Cheque was deposited in another Bank Account and Im sure the Affidavit mentioned the Cheque Number, as any strong affidavit should).
Maybe the officer didn't thoroughly trace the Transfer between two bank accounts and assumed the TRANSFER IN to be a transaction from an unknown source. Im also assuming you didnt explain this NEFT transfer in your LOE. Please correct me if any of my assumptions are wrong.
With all this being said, you do have a good case. Arrange proper documentation for this NEFT transfer and raise a CSE immediately. If you have a consultant, perhaps they can give you better advice on this matter too,