Suppose you deposit Rs. 1000/- as TDS in your case. Then you can show the party of whom you deducted TDS as Debtor for the amount of TDS Deducted i.e. Rs. 1000/- and claim from that party.
There is no need to book any expense or write it off.
As you have already paid Rs. 50000/- to that party and it can also claim Rs. 1000/- as TDS amount in its ITR. So there will be no problem and that party will give you refund of TDS amount.
Take it in another way, u were supposed to pay 49000/- to that party but u made excess payment of RS. 1000/- to it so you can show as debtor. Dnt consider diff of 1000/- due to non deduction of TDS. consider 1000/- as excess payment.