The registration on the future test does, however, have an immediate effect as you correctly pointed out. It means all supplies after the date the registration should be effective are deemed to include VAT, whether explicitly charged or not.This future test is really to catch substantial orders. Consequently you must notify HMRC within 30 days from today and you must be registered for VAT from today. The VAT number will be issued later.
While it is tempting to issue VAT invoices with ‘VAT number applied for’ instead of a VAT number, this is technically in breach of the law. No mention can be made of the amount of VAT charged unless the trader is registered, and at the date of issue of the invoice, you are not.
Therefore you can’t charge or show VAT on your invoices until you get your VAT number. However, you’ll still have to pay the VAT to HMRC for this period. You should increase your prices to allow for this without specifically stating that the amount charged is VAT and you tell your customers why. Once you’ve got your VAT number you can then reissue the invoices showing the VAT.