I had a similar original issue, and while I was able to match the Sales Receipt to the invoice and apply the payment, it's still adding the income from the Sales Receipt on top of the invoice total.

Eg. My project invoice is for $5,000, I sent a payment link asking for $2,500. I matched & applied the $2,500 Sales Receipt and it shows correctly as a payment on the invoice. But the customer/project shows $7,500 in sales. How do I fix this?