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Buy nowI have additional information to share regarding your concern, @coastalcanvasoba.
By deleting the sales receipts, this will simply unlink the bank deposit in QuickBooks Online (QBO). After deletion, you can proceed to Option 2, where you can select the retainer item and apply it to your customer's invoice.
Option 2: Invoice customers for deposits or retainers
For detailed information, kindly visit: Record a retainer or deposit.
Moreover, you may also want to check out this article to learn how to find payments you expect to see in the Bank Deposit window in QuickBooks: Find missing payments you want to deposit in the Bank Deposit window.
Kindly add a comment below if you have additional QuickBooks-related queries. I'm sure to circle back and assist you the best as I can. Take care.