The right to deduct VAT with a duplicate invoice depends on the reason to issue
The moment at which the payment of duplicate invoices is made is determined by whether a business has received the original sales invoice and the invoice has been recorded in its accounts. Taxpayers still had doubts when they could deduct VAT from duplicate invoices. There are two possible solutions.
The first applies if a copy of the invoice intended for the purchaser is destroyed or lost before it is received by the purchaser. In such a case, obtaining a duplicate invoice has the same effect as receiving the original sales invoice. This will therefore in most cases give rise to the right to deduct VAT (according to Art. 86 Paragraph 10b Point 1 of the VAT Act). Thus, in such situations, the most common deduction is possible in the accounting period of the duplicate invoice (see individual tax ruling issued by the Director of the Tax Chamber, Warsaw, No. IPPP1/443-1082/14-2/JŻ).
Source: Wydawnictwo Wiedza i Praktyka Sp. z o.o. (July 2015)