Hi heartmeat
From an API perspective, sending a customer payment to a company file only applies the payment to the invoice and closes it. There’s nothing in how the payment comes through the API, that influences whether the payment is marked as “reconciled” in the bank account or not.
I’m wondering if this particular client of yours has signed up for Bank Feeds? This is a reconciliation tool which can mark transactions as ready to be reconciled, but its completely separate to the API functionality.
