That's what I did too when I first started business. In these days, cashflow is king and the sooner you can get an invoice out, the sooner you are likely to be paid. If you have to replace it on receipt of the money with an invoice showing your VAT nr, small price to pay for getting the money in quickly.
Am sure your accountant would have mentioned it but for traders / companies doing less than 1 million turnover per annum you will only have to remit VAT on receipt of moneys, i.s.o. remitting VAT on issuing your sales invoice