Hi Dave - without seeing your books I can only talk in general terms. I'm also assuming you are on standard VAT and not the Flat Rate Scheme.
Under invoice accounting, when you create an invoice or enter a supplier bill, the VAT element is put to the VAT control account and so at the end of the quarter, the balance on that account will represent the VAT that's shown as payable on the VAT return.
Under cash accounting, when you invoice or bill the VAT is put to the VAT cash control account and sits there until the invoice/bill are paid or part paid, at which time the system automatically transfers the VAT on the payments from the cash control to the VAT control account. So again the balance on that account at the quarter end will represent the VAT per the return and the balance sitting in the cash control will represent the VAT on unpaid invoices less unpaid bills at the quarter end.
So if you've created invoices and bills in your books under invoice accounting but should have used cash accounting then perhaps a short cut way of dealing with the correction is to change to cash accounting and then delete and re-enter any invoices and bills unpaid at the quarter end?
This is only a guess as I've never actually done it and I know from experience of bookkeeping systems that they quite often don't follow the user's logic in dealing with changes.
If any of your income and expenditure has been created from bank or cash transactions then they should remain unchanged as the invoice/cash take place at the same time.