If you create a credit memo using "copy document from a posted sales invoice" you get the fields "Applies-to Doc. Type" and "Applies-to Doc. No." filled in the credit memo.
On posting the credit memo the open entry for the sales invoice gets closed (and also the credit memo).

The same should happen for prepayment invoices / prepayment credit memos
If a user has to create a prepayment credit memo then it should be checked whether the prepayment invoice is still open. And if this is the case the open prepayment invoice should get closed automatically.
This should at least work in 1:1 scenarios with not partially applied invoices, but ideally also in case the CM is for more than one INV.