Sir, before the vehicle leaves your factory premises the invoice copy should also be carried by the transporter. At that time if the invoice value is say ₹ 120000/-. And by the time the material reaches your Delhi customer, some quantity of material in the truck is lost. So the invoice booked by the customer in his books on accepting the material would be of lesser value say ₹ 180000/-. Since he has accounted the transaction for a lesser amount, he is in a position to issue Form C of a lesser amount. In such case the payment received by you will be less. Hence the customer account maintained in your books won't tie up with the invoice value. Hence you will have to pass a journal entry for loss of material in the transit. By passing the said entry your account with that of your customers account get tie up. In this scenario the Form C issued by your customers, the value in it would definitely tie up with your books.
Now coming to return filing part. A common concern is that say your sale took place in April ending and you have filed your return for April and after doing so you were informed by your customer that the quantity received is less and that he will issue forms accordingly. This creates issue for you. In such cases you have to revise your return with the revised amount after netting with the loss in transit value. This will solve your issues as described in your query. In few States Annual Return provision is there which helps the assesse to shown final amount in his return. Thanks.