A sealed record of the number of prisoners on departure.
(I have the Australia Almanac and it's full of interesting tidbits. One of them was when I read "The English met with the Aborigines during a time of hunger .. 5 men where eaten". I shook my head briefly at the inhumanity and went on to read .. then paused, and re-read the passage again. Turns out, the English ate the Aborigines.)
Whether the Aborigines ever engaged in cannibalism was a somewhat fraught political topic in Australia a few years ago. (The answer is "probably someone got eaten by somebody at some point in the 40,000 year history of the thousands of Aborginal tribes, but you're not supposed to talk about it.")
Anyway, the story isn't about captains "recreationally murdering" prisoners, which is the kind of thing that only a tiny number of psychopaths would do. It's just about them failing to take quite as much care of them in terms of food, water and medical treatment as they really should have.
As for cannibalism, my profile info has been a passing reference to it, in jest; it doesn't concern me at all, at least not until the zombie apocalypse (if food rations run low, I might have to hunt a few zombies and raid the mall shops for flat-screens and warm Heineken!)
I'm filing this under "extraordinary claims demanding extraordinary proof" for now.
The wealthiest and most powerful families of that era, or any time before 20th century, had difficulty identifying kins and heirs. The whole study of Genealogy (and, perhaps the institution of marriage!) was created for the secure identification of blood relatives and safe transfer of property.
Even visual identification is spotty when IDing strangers.