QB has duplicated some of my invoices when a customer pays the invoice in two stages/amounts. This has caused the VAT owed to double on the return that I can't change.

Hi there, @richsimmons,

I am here to help you correct your invoice payments in QuickBooks Online.

Before anything else, may I know how did you apply the payment? Did you do it using the Receive Payment option or through a deposit? Any details about this will help me narrow things down.

A duplicate invoice may attribute to an overstated income on your books. To correct this, you'll need to delete the other transaction then apply the payments to the original one.

To delete the invoice and its payment, perform the steps below:

1. Open the invoice or payment transaction.
2. Click More at the bottom.
3. Choose Delete.
4. Select Yes to confirm your action.

To apply the partial payments in QBO, follow the steps below:

1. Click the Create (+) icon.
2. Choose Receive Payment.
3. Enter the customer name.
4. Put a checkmark on the original invoice.
5. On the Payment column, enter the partial payment amount (see screenshot).
   
6. Click Save and close.

The status of the invoice will automatically change to Partially paid after following the steps given above.

To get an in-depth information about paying an invoice, you can refer to this article: Record customer payment in QuickBooks Online.

Please let me know how this goes. I want to ensure everything is all set on your end. Have a good one!