Hello there,

If you record a bank deposit make sure that it is affecting AP to be able to pay the bill. You can follow these steps: 

1. Go to + New option.
2. Click Bank Deposit.
3. In the Account drop-down menu, choose the account where you got the refund.
4. Fill in the needed fields.
5. Click Save and Close. 

After that, proceed to pay bills. Here is how:

1. Go to + New.
2. Choose Pay Bills.
3. Select the bank deposit you just created. You will see the amount of the vendor credit in the Credit Applied field. The Total payment should be $0.00.
4. Click Save and Close.

For detailed information, refer to this article: Enter a refund from a vendor.

I will leave these articles for future purposes:

• Enter and manage bills and bill payments in QuickBooks Online.
• Automatically match QuickBooks Bill Pay transactions.

Feel free to post here again if you have further QuickBooks-related concerns. We are available 24/7 to lend a hand with each of your queries. Stay safe!