Cross charge credit memos against paid invoices

I have a problem that occurs when cross-charged costs are recalculated after an intercompany invoice has already been sent - for example, when a rate or burden schedule is updated.  Projects makes a reversing and a new cost distribution line.  When intercompany invoices are generated, there are credit memos to the original invoices, and a new invoice for the new amount.  If we have our AR transaction types set up to 'allow overapplication', the credits go onto invoices that have already been paid.  If we don't allow over application, the invoices won't transfer from PA to AR.  Neither is a good situation.  Ideally,