You would need to create a deposit for the correct check , then unlink the check that was accidentally deposited from the other payments so you can record your deposit correctly. Let me show you how.
First, record a deposit:
Next, unlink the check that was accidentally deposited.
You can also read this relevant article for future help: How to Record Bank Deposits.
If there’s anything else I can help you with, please post again.
The new check is also in a deposit linked with other payments, will this be an issue?
Thanks for getting back to the QuickBooks Community, courtney6.
Allow me to step in and help provide some additional information about the deposit linked with other payments in QuickBooks Online (QBO).
QBO has automation features where it will automatically applying for payments. Let's make sure this feature is turned off on your QuickBooks settings.
Let me walk you through the steps:
For additional reference, you can check this article: Apply a credit from an overpayment.
Once done, you can follow the steps provided by my colleague on his post above to deposit the linked on the correct payment.
This will get you on the right track. Please know that I'm just a post away if you have other questions about the deposit payment. Wishing you and your business continued success.