Update iPhone/LocalNotification/plugin/LocalNotification.m

To clear all notifications, just alter cancelAllNotifications fron LocalNotifications.m file adding:
    [[UIApplication sharedApplication] setApplicationIconBadgeNumber: 1];
    [[UIApplication sharedApplication] setApplicationIconBadgeNumber: 0];

before [[UIApplication sharedApplication] cancelAllLocalNotifications];

I hope, that solution can help.