Avi's novel is about changes of all shapes and all sizes, transformations of all kinds and degrees. Charlotte is a proper young girl, but then she's dressed like a boy. The sea is calm, and then it's stormy, but wait, it's calm again. And hey, Zachariah is dead, but now he's alive! Do you see a pattern here? We thought so. In The True Confessions of Charlotte Doyle, changes happen to people, to places, and to things. To everything, in fact! We might conclude, then, that the novel wants us to see that change is a part of life. Some is good, some is bad, and some is ugly. The important thing to note, though, is that whether we like it or not, change happens.
Charlotte's personal transformation is the catalyst for a larger change on the Seahawk: the overthrow of Captain Jaggery.
Some change is good and some change is bad. It really all just depends on the context.