You can process a refund for the chargeback you've received, Alenyushka. I'm here to help you through the process.

Since the payment has already been applied to the invoice and reconciled in June, you must create a credit note for the chargeback received in October. This way, you don't need to unreconciled the transaction and seamlessly return the charge back.

Here's how:

1. Select the + New icon and select Credit note.
2. In the Customer field, choose the appropriate customer.
3. Enter the Credit Note Date, Amount, Tax, and Product/Service 
4. Click Save and close.

Once done, you can now issue a refund to the customer. To do so, follow the steps below:

1. Go to the + New and select Expense.
2. In the Payee field, select or enter the desired customer.
3. In the Payment Account field, select the bank that is being refunded.
4. Choose Accounts Receivable account in the Category field
5. Enter the amount of the refund in the Amount field..
6. In the Tax field, select the appropriate Tax (not inclusive/exclusive of tax).
7. Click Save.

Then, do a receive payment so the balance should be zero.

1. Select the + New and click Receive payment.
2. Choose the Customer and select the Payment method and Deposit to.
3. The balance should be 0 as they will cancel each other out.
4. Select Save and Close.
5. If you have Online Banking, go to Transactions and match the record found on the Bank transactions page.

For more details about the process above, see this link: Record a customer refund in QuickBooks Online. Then click the Customer refund if the invoice has been paid section.

Additionally, you can browse through these articles about fixing issues when reconciling in QBO: 

• Fix beginning balance issues if you've reconciled the account in the past QuickBooks Online
• Undo and remove transactions from reconciliations in QuickBooks Online

If you have any additional questions about recording refunds in QBO, please feel free to leave a comment. I'm here in the Community and would be happy to assist you!