How do I treat bank deposits when the corresponding invoice has been marked paid manually?

Hi, Ishort. I've got your back in reconciling your account.

In QuickBooks, you'll want to link your bank deposits to the appropriate invoice to keep your records accurate and prevent errors when it's time to reconcile your accounts.

Once the invoice payment is already recorded, you can only void or delete the transaction so you'll be able to link the bank deposit to an invoice. To do so, follow the detailed steps below.

To void/delete transactions:

1. From the left pane, go to Sales and then select the All Sales tab.
2. Find the transaction in question and then click the triangle ▼ button from the Action column, select View/Edit to open the transaction.
3. Select More in the footer. Then select Delete.
4. Click Yes to confirm.

Next, let's match the invoice to your deposit in the banking page:

1. From the Banking page, select the bank and look for the deposit in For Review.
2. Click the deposit and select Find match.
3. Filter the Date range that includes the date when the invoice payment was created.
4. Check the Payment and then click Save.

Lastly, we can find the deposit entry on your bank register to your invoice in your QuickBooks: 

1. From the left menu, select Accounting and click Chart of Accounts.
2. Look for the account you deposited the payment to, then select View Register.
3. Click the deposit and hit Edit.
4. From the Bank Deposit screen, scroll down to Add funds to this deposit, then find the fund you need to edit.
5. In the Received From column, search and choose the appropriate customer name.
6. From the Account column, choose Account's Receivable, then tick Save and Close.

You can reference this article to know more when to void or delete transactions in your account: Void or delete transactions in QuickBooks Online.

Also, I've added a helpful article that will guide you in linking a deposit to an invoice in QBO: How to link a deposit to an invoice.

I’m also attaching this link that you can use for future guidance in matching your bank statement and reconciling your account:

•  Reconcile an account in QuickBooks Online.
• Download, Match and Categorize your Bank Transactions.

Keep me in the loop if you need further assistance managing your invoices and deposits . I’m always around to assist you.