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.
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.