QBO is sending invoices to clients with their standing credit in the "pay now" field

Thank you for reaching out to the Community, @Bry!

With regard to your paid invoices, the emails are not customizable. This means we won't be able to change the remaining credit and show the invoice amount. However, they would be able to see the invoice amount once they click the Pay Now button. I attached a screenshot below for your reference.

You can also send a payment receipt instead of paid invoices to avoid confusions. Open the payment transactions, then Save and send.

I added this article on how to properly record advance payments in QuickBooks Online: Record retainer or deposit.

You can always reach us back for further QuickBooks concern. Have a great day ahead!

After doing some additional testing I found a bug in QuickBooks that is partly to blame for this problem.     It would appear ONE method of creating invoices triggers the credit notification and window whereas creating the same invoice using a different method does NOT show an existing credit (nor does it trigger the auto apply credit function)

Lets assume client has $1000 credit on their file from a previous overpayment.

If I create an invoice using this method : [Customer >create invoice> add time (right column)];  then quickbooks alerts me of a credit and and/or auto applies it.

However if I create the same invoice suing this path: [sales > all sales > unbilled activity > create invoice]; then QuickBooks fails to apply a credit, fails to tell me a credit exists, and fails to show the available deposit in an options box near the bottom of the invoice window.