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Post a Debit note to a customer account

I charge a customer say 28 invoices which comes to £3500. He then deducts £1600 for a yearly system usage fee and raises a debit note, sending me the balance of the payment of £1900. In other accounts systems I would simply create a credit note and hold it on their account. I would then allocate the 28 invoices and the credit note to the payment received…simple.
Is their a way to put a credit note on a customer’s account that is bigger than any one invoice? If not, then I don’t know how I can allocate the above. I can’t pay it off by putting it in the “opening credits account” because you can’t properly allocate it (because of the random value of actual invoices.). Any ideas - or maybe a feature request to post credits directly to the customer account.

You would create a new bank account. Enter a transaction to pay the 28 invoices. Then create a transaction for the amount they deduct. Then the balance will be the money received which you would tag as a transfer to your proper account where the transaction appears.

I’d do it the way Paul suggests, as the debit you receive from them isn’t really a credit note as such, it’s more of a contra invoicing situation where you’ve charged them £3500 for sales, they’ve charged you £1600 for purchases, and rather than both pay each other in full you just transfer the difference.