Turns out is is as simple as calling:
tree.jstree("refresh");
At version 3 you can reload the tree :
$('#treeId').jstree(true).settings.core.data = newData;$('#treeId').jstree(true).refresh();
var tree = jQuery.jstree._reference("#files");tree.refresh();
or
var tree = jQuery.jstree._reference("#files");var currentNode = tree._get_node(null, false);var parentNode = tree._get_parent(currentNode);tree.refresh(parentNode);