Symptoms
There is a payment in Hold status, it was not released in BA due to some reason (can be a system crash for example) but actually request to processing center has been sent and processed successfully. It is possible to delete such payment. On clicking Delete button no requests to the processing center are sent. This results in the inconsistency - processed payment on the payment gateway and no payment in BA.
Cause and resolution
The issue was decided to be treated as a feature request with id #PFR-378 ("Do not allow to delete payments that may be still in processing on the payment gateway"). Basically the root cause here is to be fixed - e.g. avoid system crash, so that BA could receive correct payment status right away. The basic recommendation that can be given is not to cancel the payments that are oh hold and did not fail due to obvious reason (no failure reason on E-transaction tab), but to check the payment status on the payment gateway and only then cancel the document.