Dude when the phone rotate android will destroy your app and recreate it again...here you are right. However while this is happening the system will call onSaveInstanceState() method, so here you can save all your current instance and then get them back at on Create() method
Example:
// to save instance before your activity is destroy
public void onSaveInstanceState(Bundle savedInstanceState){
super.onSaveInstanceState(savedInstanceState);
{
savedInstanceState.putBoolean("yourKey", timerRunning );
}
}
}
// then retrive it on your onCreate() method if(savedInstanceState != null){
// Restoring all Instances
timerRunning = savedInstanceState.getBoolean("yourKey");
}
But if you dont like this method you can always set your activity not to recreate himself at onConfiguration Change by adding this:android:configChanges="orientation|keyboardHidden|screenSize"
in your manifest inside your activity element, this method will solve also your problem and save you some time coding :)
Hope it help