Whittle's journal of the events aboard the C.S.S. Shenandoah have a dearth of entries between the 25th of January, 1865 until the 20th of the following month. Tensions were high aboard the vessel due to American consulate activities and the fact that, well known to the officers, the ship had taken on forty "stowaways" to increase the effective complement of the vessel. The question of safely clearing Australian waters must have been uppermost to the command, the sinking outside of a French port of one of the other crusiers being a witnessed memory to some on board the "Shen". I'd wager those tubes aboard were charged and shotted.
Please note Whittle's entry for the 25th of January and realize that it had to have been written some time after that date. My guess for the lack of journal entries during the period in question is due to the journal either being hidden in case of hostile boarding or its being bound and weighted for rapid disposal in case of same.