We'll have to match the recorded VAT payment to the actual bank transaction to clear it out, ubusi. I'll guide you on how to do this below.
To prevent duplicates, you need to match the downloaded bank transaction to your existing VAT payment entry in QuickBooks Online (QBO). This will make it easier for you to reconcile your account. Here's how:
For the complete guide in reviewing downloaded bank data, please see this article: Categorise and match online bank transactions in QuickBooks Online.
Additionally, I'd encourage you to reconcile your account regularly (monthly) to ensure they're balanced and accurate.
If you need further assistance with managing VAT payments and banking files, please reply to this comment. We are here to help you further.
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