It's clunky, but the best way I'm aware of is an interco JE.
If someone was supposed to pay an invoice on Subsidiary A, but they paid a bank account on subsidiary B, you do an interco JE with the following distribs:
Sub A:
DR Interco Acct
CR Accounts Receivable (note the customer in the Name column
Sub B:
DR Cash account money actually went into
CR Interco Acct
Then apply the JE to the invoice. If you're dealing with foreign currency, you'll have to double-check if that creates the requisite realized gain/loss. If not, you might have to kind of follow the same concept, only do a payment through a 'clearing' cash account and then do an interco JE behind the payment.
Last, but not least, be aware that any resave of a JE applied to another document (even if you don't change anything) unapplies it from that document.