Paid the same invoice twice, Vendor Center showing negative balance, how do I reduce that balance as I use the credit at the vendor

I'm here to help you handle the negative balance showing in your Vendor Center, @McMillanClerk.

We can record a refund you received from a vendor. To proceed, create a deposit for the vendor who sent the refund check:

1. Go to the Banking menu, then choose Make Deposits.
2. If the Payments to Deposit window appears, click OK.
3. In the Make Deposits window, choose the Received from drop-down and choose the vendor who sent you the refund.
4. In the From Account drop-down, select the appropriate Accounts Payable account.
5. In the Amount column, enter the actual amount of the refund.
6. (Optional) Enter a memo, check number, payment method and class.
7. Click Save & Close.

For additional information, please see this article: Record a vendor refund in QuickBooks Desktop. 

If you have further concern about handling twice paid invoices in QuickBooks. I'll be happy to help you. Keep safe!

Will doing this impact my bank reconciliation? I did not receive any cash from the vendor so I'm questioning whether selecting "deposits" would be the correct move.

Welcome to the QuickBooks Community, @McMillanClerk.

Let me share further insights on how to handle a negative balance in the Vendor Center. 

There are two ways to remove vendor credits in QuickBooks Desktop (QBDT). You can either apply it to a bill if the credit itself existed in real life transaction. That way, it will reduce the negative balance in the vendor's account. 

Here are the different scenarios on how to record a vendor refund and apply them to bill payments: Quick guide in recording refunds you received from a vendor.

If your predecessor accidentally recorded the payment twice, you can simply open again the transaction and delete it. Here's how:

1. Go to the Vendors menu and select Vendor Center.
2. Look for the name of the vendor, then click it.
3. Search for the duplicate payment and double-click it to open.
4. Select the Delete button and click OK.

Moreover, you can run several financial reports in QBDT to tell where your company stands. These offer critical information about your business and finances.

Please let me know if you have any other vendor credits concerns or other questions related to QuickBooks. I'm always here to provide further assistance. Have a good one.