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Hello, I am Keith, one of the experts on Just Answer, and pleased to be able to help you with your question.
Firstly the VAT charged by Customs on importation may be reclaimed as an input tax on your quarterly return. The VAT you charged the customer on sale must be used to reduce your output VAT in the period that the product is scrapped. The scrapping balance once the VAT has been stripped out is chargeable to the profit and loss account. Of course your VAT account will be skewed over this transaction, but this cannot be avoided.
I do hope that you have found by reply of assistance.
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