Hi David
Yes - if a credit note for the same amount as the invoice has been entered onto the system, when you go to 'make payment' in the top panel will be the invoice, in the lower panel will be the credit note, so one will offset the other if selected accordingly, so the relevant date just needs to be checked, then save and close.
If sending to the client, QuickBooks just marks the invoice as 'paid' in the crediting off process, so I usually go back into the invoice first and add another line explaining that the invoice has been offset against credit note number 'xx' and re-save it. If you do this, then at least on your system, and on the clients copy of the invoice, there is relevant information as to 'how' its been 'paid'. Likewise, I will put on the credit note which invoice number it's credited, or why there is a credit.
Yes this is reversible, for example, if you agreed with the customer to credit off the invoice, then he decided to pay you afterall, you could call up the credit note again and 'up-apply' it, which would then leave the invoice unpaid again, so that payment could be applied and the credit note deleted - but obvioulsy you would only consider doing this if you haven't sent your customer the credit note.
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