I'm here to share additional information to help you delete your duplicate payments, @Andrew93.

Let's start by making sure that your QuickBooks software is updated to the latest version. Here's how:

1. While on the No Company Open screen, go to the Help menu.
2. Select Update QuickBooks Desktop.
3. Choose the Options tab.
4. Select Mark All and then click Save.
5. Go to the Update Now tab and select the Reset Update checkbox.
6. When you're ready, select Get Updates.

Once completed, let's close and reopen QuickBooks Desktop to make sure that all components are updated. Now, let's run your Transaction List by Customer report. This is to review if the other invoice payment is still applied to the invoice. 

On the other hand, you can delete all the payments that have been made then re-apply and deposit them. Let's delete the deposit first so we can completely delete the invoice payments. Here's how:

1. Click on Lists at the top menu bar.
2. Go to the Chart of Accounts tab.
3. Select the bank where the invoice payments were deposited.
4. Locate and open the deposit. 

   

5. Press Ctrl+D on your keyboard.
6. Click on OK.
7. Select OK when asked to delete the transaction.

Now, you can re-apply the invoice payments and deposit them. You can read through this article for more detailed instructions: Record an invoice payment.

Feel free to get back to us here if you have other questions about managing your income-related transactions. I'm always here to help.