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I'll help with your question about vendor refund as well as making the vendor's balance zero.
Make sure that the account used in the deposit is not the Accounts Payable account. Otherwise, the vendor's balance will not zero out. Here's how to check:
Aside from that, you can also run the Vendor Balance Detail report. This will give you a list of all transactions that are affecting the vendor's balance to determine why it's not zero. Just go to the Reports menu and type in the name of the report in the Search bar.
You can also check out this article on how to add a filter to it: Customize Reports in QuickBooks Online.
Please don't hesitate to reach out to us again or add a reply below if you need anything else. We're always here to help.