Sadly in the absence of Official Records one has to go with what they can find. It is like investigating a crime scene. You very rarely every find a written confession at the Murder scene. You have to build the criminal case upon the fragments of evidence that you find from different sources.
Mallory's destruction of the CSN records sadly reduces us to drawing upon these secondary sources as our primary documentation. The Deck Log of the CSS PONCHARTRAIN may yet be hidden in some closet or archives. But since the Mississippi River was already blockaded by the time of the PONCHARTRAIN destruction the question is where would they have been sent, if they could not be sent to Richmond because of the Blockade.