You have at least 2 options I can think of at the moment:

#1 - continue to issue credit notes in your system, but don’t send them out or 
pay them with a check. When you have the next positive invoice, ‘pay’ a portion 
(or all) of that invoice with the credit note. Simply process a payment, select 
the credit note line and an invoice line you want to apply it to in the top 
part of the window. GnuCash will offset the invoice with the credit note for 
you. If the credit note is more than the invoice, it will retain the left over 
as remaining AR credit to be used on subsequent invoices. You can see the 
customer’s balance any time either by looking at an AR aging report, or a 
Customer Report. Outstanding credit notes appear in the Invoices Due Reminder 
window.

#2 - If your client regularly pays in advance based on an estimate and you 
invoice later, instead of applying the payment to an invoice, apply it to a 
Liabilities:Customer Deposits account. Then when you create and post the final 
invoice, process a payment for it from this account. You could keep a separate 
deposit account for each customer but that might get tedious. You can run a 
report on the account sorted by payee to show that info and even keep that 
report open in a tab if desired, choosing to refresh it as needed. If this 
might only happen for pre-paid expenses, then you can still use this method, 
but only for the pre-paid expense part, which you could (or not) choose to 
invoice separately.

Regards,
Adrien 

> On Jun 26, 2019, at 1:46 PM, Eric Rathhaus office <e...@ewrlaw.com> wrote:
> 
> Hi - I have a client for whom I have many jobs.  On some of these jobs, the 
> client prepaid expenses that I did not use.  In the past, I’ve always created 
> a credit note for a refund and sent the client a check.  However, my client 
> prefers instead that I credit this amount towards future work.  I’m not sure 
> how to accomplish this cleanly.  I could keep a running total of the amount 
> and discount from the total prepayment until it’s used up.  But this seems 
> clunky and maybe not the best practice.  Any other suggestions on how to 
> account for the refund against future work?
> 
> Kind regards,
> 
> Eric W. Rathhaus


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