Thanks for getting back to us and providing an update, @kvngrffn.

When turning off the Automatically apply credits feature in QuickBooks Online (QBO), it will not affect transactions that are already applied. Thus, when you create a new Credit memo, this will not apply to any open invoices.

To find and reverse the incorrect application of the credit against the wrong invoices, here's what you'll need to do:

1. Go to the Sales menu at the left pane, then select Customers.
2. Click on the customer's name you want to open.
3. Go to the Transaction List column, then filter the transactions to Credit memos.
4.  Double click the credit to open the transaction.
5. Click the payments made at the upper right corner and select the linked transaction.
6. Make sure that the amount received is zero.
7. Click More, and select Delete.
8. You'll now have the unapplied credit.

I've added this resource if you need help on how to handle a customer credit or overpayment in QuickBooks Online.

For additional reference, visit this article on how to enter and apply credit memos and delayed credits in QuickBooks Online, which you may find helpful. 

Know that you're always welcome to stop by the Community if you need anything else. I'm here to help. Have a fantastic day!