How do I deal with an invoice paid twice by the customer as I can't put it to the same invoice number?

Hi there, Gillian. Thanks for sharing the detailed information about your concern.
 
You can create a refund receipt transaction to deal with an invoice that was paid twice by your customer, if you have returned the money to them immediately.
 
This will offset the excess amount you received in your QuickBooks record, balancing to your real-life bank entries.

Here's how:

1. Click the (+) New icon.
2. Choose the Refund receipt option below the Customers column.
   
3. Select your client's name in the Customer field.
4. Enter the correct Refund Receipt Date.
5. Pick a Payment Method and choose an account in the Refund From field where the amount will be debited.
6. Type in the information of the Service Date, Product/Service, Amount, and other necessary details for your refund record.
7. Once done, click on Save and close.
   

Another way around is to create delayed credits for them. This works if your customer prefers getting a credit to lower the cost of their next purchase. You can read this article for more information: Handle customer adjustment notes and delayed credits in QuickBooks Online.

Feel free to leave a comment below if you need further clarification. We're here to assist you.