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Accounts receivable is the default account in QuickBooks used to track money owed on open invoices to customers, once this is paid, the balance is then cleared from this account.
There are two types of accounting methods - cash and accrual basis Depending on which you have selected in the settings, the invoice payment will post as sales income either on the date that this was raised (accrual accounting) or on the payment date (cash accounting).
As the transaction in the bank is a payment, it's correct that this should post as sales income. If you've already raised and marked the invoice as paid, you can instead 'match' the transaction in the bank to this, to prevent duplication.
To fix this, you can go to Banking > Categorised > Locate the transaction > Select 'Undo' > Scroll up and click on the 'For review' tab - you should see that the transaction re-appears listed here. If there is no automatic option to Match in the Action column, please click into the transaction and select 'find match'.
We can not advise which VAT code to use for the transaction itself we do have a list of common VAT codes here and when to use them. If it should not show at all in the VAT return you can use t he no vat code. The transaction which posts to the sales account, what type of transaction is it, bank deposit, transfer,invoice, sales receipt?is there a product or service attached or is it an income account? By payment coming over do you mean in the banking section and then you are matching it to an existing transaction or are you adding it in there?Could you post a screenshot of one of the transactions as an example?