Hello Ishana,
Your post made me wonder whether it was possible to select a Vendor and some invoices and the blank out the vendor code for a miscellaneous payment to the same payee. It isn't (at least not in AP V8.1D (120814)) and I doubt in earlier versions.
Is the cheque in the Check Register? Can you find the transactions in the GL? (To locate a transaction in Ledger where you don't know the account, print-preview the entire GL detail listing and use the preview window's "Search" function (the binoculars at the top of the screen) to look for something identifiable in the transaction like the vendor name.)
Is it possible that the client has forgotten the vendor code and that all this activity took place on a different vendor?
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Andrew Bates