Hi, @OIAI.

You can use a credit memo as payment for another transaction, you can check your invoices and compare them to the payments for you to trace credits.

You can refer to this article to know how to enter and apply a credit memo in QuickBooks Online. Enter and apply credit memos and delayed credits in QuickBooks Online.

I’ll be glad if you can tell me more about what happened before you turned off the auto-apply credit for me to give you additional information. Have a nice day!