hmm, something like this (didn't tried it yet):

//from main programm (on windows, I am sure on Linux you can find something
similar to Start):
Runtime#exec("start java <myUpdateProgramm> -Dpath=<mainProgrammPath>");
System.exit(0);

//update programm
readNewVersion();
 int errorCount = 0;
while(true) {
   try {
        //try to save update
        saveUpdate(getUpdatePath());
        System.exit(0);
   }
   catch(UpdateFailedException ex) {
       //main programm still running?
       if(errorCount++ > MAX_ERROR_COUNT) {
           //something goes wrong
           System.exit(0);
       }
       Thread.sleep(5000);
   }
}

Andrey