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Hi Karen
QuickBooks makes it easy to 'change' the VAT on an invoice and I've done this on occasions, when I've not know whether an invoice has VAT on it or not, so I've put it as O or Z, then gone back and changed it when I've received the invoice.
If the invoice is dated in a previous VAT quarter, QuickBooks will pull the change through on the VAT Exemption report in time for the next return. Again, I've done this when it's the quarter before the current one, and it doesn't cross over a year end, but this is what you have to consider.
As your invoices are for much more than one quarter before, they will also, no doubt, cross the year end, which the Accounts will have been drawn up for.
My advice would be to have a word with the clients accountant, and see what they advise you should do.
If they want you to put it all in one quarter/year, the way to do this would be to raise another supplier bill with nil value with just the VAT claimed - a description can be given on it as to why the bill has been raised. In desktop version, the VAT is claimed by using the Z code, a nil value, then altering the VAT box at the bottom by the amount you're claiming. In the Online version, it won't let you raise a nil value line, so you have to put it at 1p, then a second line for minus 1p (to cancel the above line) then this will then 'open up' the VAT box for putting in your amount to claim.
Hope that helps.
Carol
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