We often get our clients to mark an invoice as paid for their own debtors control purposes, however tell them not to touch the bankfeed, as we would deal with that on their behalf for VAT return preparation.
However lets say two customers have the same amount of invoice, and only Customer A has paid and the client has marked this invoice as paid. When we go to import the bankfeed, the system automatically tries to re-allocate the payment received against Customer B invoice, as it's matching the amount and not the actual customer name. Even though only one invoice has been paid on that banking date.
The only way to avoid this is by ignoring the transactions before importing the bankfeed, which is time consuming.
There should be away that the bankfeed can recognise the outstanding debtors if the client is using the add payment function and assigning the date against when monies came through the bank, as only one banking entry has actually been made.