Last quarter I switched from cash accounting to standard VAT scheme. I reconciled the final VAT return in the cash accounting scheme and all was fine.

Here is my problem - Since doing that return I have raised credit notes for a couple of invoices that were dated in the last quarter. They had not been paid, therefore did not appear on the (cash accounting) VAT return. I allocated the credit notes directly to the relevant invoices and now those credit notes are appearing on the new VAT return, therefore reducing our output VAT. This should not happen because they were never added to output VAT in the first place.

I hope that makes sense! All I need to know is, how do I stop those credit notes from being flagged for VAT and reducing the output VAT, or is there a manual adjustment I should make?

Thanks you.