You may use the VAT Cash Accounting Scheme. You may have invoices and standalone credit notes that have different VAT rates. Allocating these gives the following:

In this scheme, VAT from invoices goes to a holding account. When you receive payment, it moves to VAT accounts for tax reporting. If you issue a credit note without payment, it cancels VAT. Different VAT rates leave some value in the holding account.
An example
You issue an invoice for €100 plus VAT at the standard rate of €20. The customer pays the invoice and the receipt appears on your VAT Return. The customer then returns the items because they were faulty, for which you issue a credit note. The credit note leaves a debit balance of €20 in the VAT on the sales holding account.
They then place a further order for you for €120 with a mixture of different VAT rates:
€90 at the standard rate
€10 at the lower rate
€1.50 which is exempt from VAT
Total VAT €18.50
Allocating a credit note and new invoice results in a €1.50 debit in the VAT sales holding account. Credit notes aren't on VAT Returns. Therefore, it leads to an overpayment when reporting the original receipt.
To resolve this, do one of the following:
- Select No. Issue a refund for the credit note and record the invoice as paid. The refund and payment are on the VAT Return so it includes the difference. Your bank balance doesn’t change as the refund and receipt are for the same value and cancel each other outYour bank balance doesn’t change as the refund and receipt are for the same value and cancel each other out
- Unallocate the original receipt and invoice. Allocate the credit note to the original invoice. The receipt becomes a payment on account which you can allocate to the new invoice
- Manually journal the VAT mismatch from the VAT holding account to the VAT on the sales account. In this example you would post the following journal:
Ledger Account* | Debit | Credit | Include on VAT Return? |
VAT on Sales – Holding Account (2205) | 0.00 | 1.50 | No |
VAT on Sales (2200) | 1.50 | 0.00 | Yes |