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Hi I am one of the experts. Asking for VAT only invoice later is possible because registration can take time. Now, on the other hand, they should have informed you about this in the past when the invoice at first place sent to you for payment.
About different company VAT registration, this is something you need to discuss with them and deal with it according to your arrangement as you know better what is bought.
Thirdly, a proforma invoice should say on the top Proforma Invoice.
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No logically it should be the same company. You should discuss and agree on a solution with the seller.
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