phonegap/phonegap-plugins — pull request #1051 by cyerena (2013-02-27 01:23:29+00:00)
Title: 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.