You need to use JavaScript to do that.
You can create an action with Action Wizard to execute the following JavaScript which will change the color of all highlight annotations in the document (to green in this example):
this.syncAnnotScan();
var annots = this.getAnnots();
for (var i = 0; i < annots.length; i++) {
if (annots[i].type == "Highlight") {
annots[i].strokeColor = color.green;
}
}
