I had a contra entry to make where client had reduced supplier payment by amount owed to them on sales ledger.
The method told me by support was to create a dummy bank account and post both sides to this, it seems a bit clumsy, what is needed is the ability to offset between ledgers directly.
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TAS software can do this where you tick in either customers profile or the suppliers profile that either are also the other ie the customer is also a supplier or supplier is also a cutomer so a set off can be selected when allocating credits
It used to work through batch payments (You could put a payment of £0 and allocate sales and purchase items to it) These have now been seperated so cannot do it.
Just seen and voted on similar request. I have a lot of clients in airfreight sector and it is a very common occurrence in this sector.