Invoiced a Customer twice for the same product and they paid. I need to refund the money and the order was placed in a different fiscal year.

Glad to have you here in Community, Vonda.

I can provide you with some information to help you refund your customer for a different fiscal year.

In QuickBooks, the system will offset the amount and zero out the balances when you void a transaction. The previously paid sales taxes are unaffected when a sales entry (invoice) is voided.

The payment will be kept and used as credit for the next tax year. This means that voiding an invoice from a closed fiscal year will immediately apply a credit to the current sales tax filing period. With this, you can void the second invoice and give your customer a refund by creating a check with a date that belongs to the taxable period.

Here's how:

1. Go to Sales, then the Invoices tab.
2. Open the invoice you want to refund the payment for.

1. Click More action, then Void.

After that, create a check to record a refund. I'll show you how.

1. Click the + New icon.
2. Select Check.
3. Locate the customer you want to refund from the Payee drop-down.
4. In the Payment account drop-down, choose the bank account where you deposited the payment. 
5. Select Accounts Receivable in the Category column.
6. Enter how much you want to refund in the Amount field.
7. Fill out all other necessary fields.
8. Once done, hit Save and close.

For your reference, you can read this article for more details: Record a customer refund in QuickBooks Online.

In addition, you can run the Sales Tax Liability report to see detailed information about taxes you owe and why you owe them.

If you have further questions or concerns, reach back to us anytime. We're always available to lend a helping hand.

My major concern is that the revenue has already been recognized for FY22, and if I void the transaction, won't it change the amount of revenue for FY22?