Thanks for getting back to this thread, @topshelf.
Allow me to step in and help correct the Profit and Loss discrepancy in QuickBooks Online (QBO).
I appreciate the additional details you've added. In this case, since you're customer used the Undeposited funds and you processed bank deposit, it will lead to duplicate recording of the transaction which causes an over statement.
To correct this, you need to delete the deposit you've made. Then you can process bank deposit again and make sure to link your customer's transactions that were recorded to the Undeposited funds to combine payments.
To delete a deposit, here's how:
Once done, you can record a bank deposit in QuickBooks to combine payments by following the detailed steps in this article: Record and Manage Bank Deposits in QuickBooks Online.
If you need further assistance with the steps, I recommend contacting our QuickBooks Online Support Team. They have additional tools to pull up your account and do a screen-sharing.
Here's how you can contact our customer support:
That should do it! Feel free to leave a comment below if you have other questions about the bank deposit. I'll be around to help you out. Wishing you and your business continued success.