You can definitely delete the deposit that was recorded manually, @vohenningtreasurer.
If these deposits are duplicate transactions and hasn't been reconciled yet, it's perfectly fine to remove them from the bank register. This action will help ensure that your financial data remains accurate and not overstated. Rest assured, I'll be suggesting some steps to keep your records in good order.
Make sure to log in to QuickBooks as an admin user and then follow these steps:
- Go to the Gear icon and select Chart of accounts.
- Find the bank account in question, then click View register.
- Select the Funnel icon and then choose Deposit from the Transaction Type drop-down.
- Hit Apply and click the deposit transaction.

- Choose Delete and then Yes to confirm.
For reconciled transactions, you'll want to undo the reconciliation first and then follow the steps above to delete a bank record. This is to ensure that your real-time bank transactions and balance coincides with your bank statement.
On the other hand, you've mentioned that the bank added them together automatically. Have you, by chance, set up a rule to categorized them automatically? This is the reason bank transactions are added automatically to the bank register.
If this is the case, you'll need to disable the rule first and undo the categorization in the Categorized tab of the Bank transactions. Then, you can match both records from the For review tab.
- From the Transactions menu, go to the Rules tab.
- Find the rule in question.
- From the Actions column, click the drop-down beside Edit.
- Select Disable.

Once everything is in order, you'll need to go to the Categorized tab under Bank Transactions to undo them. This way, you can match the bank deposit record in QuickBooks with the downloaded deposit entry from your online banking in the Bank transactions' For review tab.


For reference about deleting records and matching transactions, please check the references below:
Furthermore, I highly recommend using this article as your guide: Learn the Reconcile Workflow in QuickBooks. It provides comprehensive information on every step of the reconciliation process, both before and after.
That will be all you need to know about deleting or maintaining deposit entries. Please feel free to ask any questions regarding keeping or removing records in QuickBooks Online, or any other relevant concerns. I will be happy to assist you further, vohenningtreasurer.