Hi,
as i understand ,it is more or less allatched with the accounting you follow. clear the inv f-54 and
Balance 1000 will be still in ur receivable from vendor logically. as mentioned one of experts , send a debit memo to vendor for payment. if it is been long follow the companies policies for write off. last if vendor pays back. Transfer entry for 1000 will be done to the vendor account and then receive the payment of 1000. then u can clear the 1000 otherwise it will be knock off with misc receipt / expenses account.
Hope i hav made u clear to some extent.. mark it helpful if it is .. rgds Gopal Rawat