Cash receipts - One payment for multiple customers

We are in the process of implementing auto cash. We have done some preliminary testing and uncovered the following situation that I'm not sure how to best handle.

A customer sends in a payment for 1,000 and there are 10 transactions, 8 invoices and 2 credit memos.

The 8 invoices will match as they belong to the customer who sent in the payment but the two credit memos will not match because the credit belongs to and was given to a different customer.

This is becoming fairly common in the pharma space as there are more and more mergers. In many cases, the original sale took place prior to a merger and the purchasing company may opt to take a deduction off the payment and reference the invoice or credit that was issued to someone else.