When clicking "Clear Configuration" the defaults.conf is not loaded, thus the defaults.conf file will be empty once saving the cleared botnet. This can be fixed by modifying configs.js (function load_bots)
if (getUrlParameter("configuration") !== "new") {
load_configuration();
} else {
load_file(DEFAULTS_FILE, (config) => { app.defaults = read_defaults_conf(config) })
draw();
resize();
$saveButton.blinking();
}
Adding the "load_file" statement correctly loads defaults.conf when clearing the botnet.