If you're cash accounting for VAT purposes and the payment on account has been VAT reconciled, then Sage may well not let you delete it anyway. I can only suggest that you take a back-up and then have a play around.
Is it possible to allocate funds so that the cumulative position is correct? In other words, if you've paid/received the money that relates to the invoices which have been incorrectly allocated, can you allocate these funds to the invoices against which the payment on account should have been allocated?
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Pearce & Co - Chartered Accountant and Chartered Tax Adviser