We frequently receive prepayments from clients before starting their work. We record these prepayments to the clients' Projects in QBO using the Receive Payments window. At this point, there is no invoice for this work. Once the work is complete, we enter an invoice. Upon clicking Save & Send, QBO used to auto-apply the prepayment credit we entered earlier, and then send the invoice. But, this is no longer happening and hasn't for a few months.

A couple of things I should point out:

1. We use extensive use of Projects, so both the prepayment & the invoice will be applied to the appropriate Project.

2. In troubleshooting, I've found that QBO will auto-apply credits to invoices in the way I described, only if I do NOT enter it under the customer's Project. But this is not where we wish to enter this since we use Projects.

Has anyone else noticed this behaving differently than in the past?