After a discussion, we decided that the best option is to reverse the "cheque" (which is really 2 cheques combined) and then re-enter the single cheque that was processed successfully by the bank.

It turns out that their previous software wouldn't allow 2 cheques from the same customer to be recorded as separate entries; they had to be totalled and entered as one transaction. Adagio doesn't have that restriction so this situation won't arise in the future,