Document doc = Jsoup.parse(htmlFile, StandardCharsets.UTF_8.name());
Elements els = doc.select("script");
for(Element element: else) {
    element.text("Text that should not be escaped. eq '&'");
}

import org.jsoup.nodes.DataNode;


element.empty()
element.appendChild(new DataNode("Text that should not be escaped. eq '&'"))