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You may have adjusted the invoice amount while receiving the payment. That's why you have a discrepancy in your income statement. With this, you can delete the said payment and record one with the full amount to resolve the difference and reconcile your account accordingly. I'll guide you through the process below.
There's no need to adjust the invoice amount while recording its payment since the charges incurred will be added in the Add funds to this deposit section while creating a bank deposit. This way, you can match it to the downloaded transaction from your bank feeds.
To correct the discrepancy, you'll first have to delete or void the invoice payment, and then next is the deposit (go to your account's register to do so).
To delete or void the invoice payment, here's how:
After deleting or voiding the invoice payment and deposit, re-create the Receive payment transaction. Then, record a bank deposit and match it to your bank feed transaction. Please see the steps outlined by my colleague above to complete the process.
Once everything is all set, reconcile your account. I encourage you to do this regularly (every month) to monitor your income and expense transactions and detect possible errors accordingly. To guide you in doing and fixing reconciliations in QBO, you may want to check out this article: Reconcile workflow in QuickBooks.
I'm all ears if you have other banking and reconciliation concerns or questions about managing transactions in QBO. You can drop a comment below, and I'll gladly help. Take care, and have a great day, AT014.