How do I correctly reflect a negative deposit due to a refund?

We appreciate you in-depth details of your banking concern. We have another way how you can split the transaction to classify the batch items in QuickBooks Online (QBO).

Since the "Apply and confirm" button is greyed out, we can exclude the downloaded transactions instead. To do that, follow the steps below:

1. Go to Bookkeeping, select Transactions, then select Banking (Take me there).
2. Select the For Review tab.
3. Choose the checkbox of the transactions to exclude.
4. Press Exclude.

The transaction moves to the Excluded tab of the Banking page. Then, we can manually record the refund in QBO. Let me guide you on how: 

1. Go to the Transactions menu on the left pane.
2. Choose Chart of Accounts.
3. Locate the account where you want to record the refund. Then, tap View register.
4. On the Date column, click the drop-down arrow and choose the Refund option. Then, enter the details.
5. Press Save.

 In the future, we can use bank rules to automatically categorize transactions from your bank by following the steps and details in this article: Set up bank rules to categorize online banking transactions in QuickBooks Online. Furthermore, after you've categorized the transactions, you may also have to review your accounts in QuickBooks to make sure they match your bank and credit card statements. For more information, go through this article for more details: Reconcile An Account In QuickBooks Online.

Know that we are always here to guide you should you need more assistance in splitting and categorizing your transactions or any banking concerns. You have a good one. 

Thank you for the detailed instructions.

I followed the first steps and successfully excluded the batch transaction from my Bank Transactions list.

However, I'm having an issue with the second set of steps.

When I view my Chart of Accounts, there is no "View Register" option for the account against which I need to record the refund. The options are "Run Report", "Edit" or "Make Inactive" (as you can see in the attached screenshot).

What other options do I have to record the refund for that account and the other deposit transactions that were a part of that batch? Should I do it as a ledger entry?

I appreciate your follow-up response, devilmaskstudio. Let me provide further input to help you categorize transactions in your company file.

When viewing registers under your Chart Accounts, income and expenses won't have this option. You'll have to record this entry to a Bank account type to enable the View Register option.

From there you can refer to the steps above on how to manually record the refund. I've included a screenshot for reference.

Additionally, you may also create an Expense or Check transaction to record customer refunds. To do this:

1. In your QuickBooks Online account, go to the +New icon and select Expense or Check.
2. Enter all information and choose an Expense category.
3. Review all details, then click Save and Close.

Once everything comes in handy, it's best to regularly review your accounts so they always match your bank and credit card statements: Reconcile an Account in QuickBooks Online.

I'll be on this thread anytime you require additional assistance managing banking transactions in your account. Keep safe!