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Buy nowIt's great to hear from you again today, cornerstonemgmtg.
I'm by no means an accounting professional, but allow me to join this discussion and share some insight that can help get you on the right track to recording this.
I wouldn't recommend creating credit memos. While these could zero out Accounts Receivable (A/R), they would also increase your income which can cause a discrepancy on your books. As was mentioned by my colleagues, MichelleT and GarlynGay, it would be better to link the deposits to your invoices.
The following steps will guide you through that process:
To find and edit the deposit
Click Save and close.
To apply the deposit (payment) to your invoice
I'm also including an article for more information about this process: How to link a deposit to an invoice
This will let you apply the payments (deposits) to the correct invoice showing as outstanding. In addition, this will also ensure that the affected accounts (bank, income, and A/R) are balanced.
However, since you've mentioned that these transactions were already reconciled, you may wish to seek additional guidance from an accounting professional. Every business is unique and they can make suggestions on how to handle this. Our Intuit Find-A-ProAdvisor site can help you to find certified professionals in your area.
Don't hesitate to reach out to me here in the Community with any additional questions or concerns you may have. Thanks for dropping in, wishing you and your business only the best.