Sales Receipt / Receive payment

Hello, MelanieDDSF! Yes, there are ways of resolving this without affecting your bank reconciliation.

There are also two options on how you can do this in QuickBooks Online, depending on what's most applicable to you. 

Firsts, Keep the sales receipt and delete the original invoice. This way, the sales receipt resolves the payment and won't affect your reconciliation since it was already deposited and reconciled.

Second option is to unlink the deposit from the sales receipt if it went through the Undeposited Funds account. Then, delete the sales receipt before linking the deposit to the invoice. Let me show you how:

1. Open the reconciled deposit.
2. Uncheck the sales receipt.
3. Scroll-down to the Add funds to this deposit section, then choose the name of the customer in the Received From column.
4. Choose  Accounts Receivable in the Account column, then enter the amount in the Amount column.
5. Click Save and close.

Once done, go back to the invoice and click Receive payment. Then, choose the reconciled deposit in the Credits section to close out the invoice. 

You can always get back here if you need anything else.