(Note: I don't have old invoices for his prior payments toward the retainage—they came as checks/cash and I deposited them in the bank immediately. They originate in QuickBooks as standalone deposit transactions.)

Your second suggestion seems the best way to go. But how would I link the deposit transaction to the specific new invoice, given that I'm assigning the entire A/R account in the Make Deposit dialog?

Thanks,
Jeff Bowman
Fairbanks, Alaska