Think about it... if they are all programs yeah you an delete them, BUT you can also save them. Why not just keep on saving a program, like you do in video games (after you have just gotten past a hard part you go and save it so if you die in the future you wont have to come back and re-do it) You could just "reload a program" I dont know i am getting more confused as i write about this... but put in your thoughts.
Hows this, the progarames save by themselves by bookmarking if you will by giving you food
Thread=the oracle and the cookies
Maybe the other Matrix's have been saved... ever thought of that? Maybe Neo has tried to save Zion a thousand times, but he is only the fifth (or sixth, I can't remember) program... great point. Maybe... well, if everything has been programmed to happen, what's the big deal about choices? Unless there are two alternative endings to the Matrix... I'm giving myself ideas just writing this! Thoughts, please.
my theory is that smithj was deleted and was reloaded but differently(neo deleted him in m1)
Agent Smith wasn't deleted but reprogrammed. His program is like a virus, that copies until he has complete control of the matrix, and he must go through Neo to become the most powerful in the Matrix