I can see this being an actual scenario or plot element in the future matrix sequels. As science progresses in the world, and as time passes, the technology has to improve, and history has to continue. Everyone would have their memory reset to a specific point in time, and the program could run all over again. Perhaps all human beings are massacred and replaced with fresh clones. After all, wouldn't it be needed to make sure that humans don't create the machines a second time, creating a matrix within a matrix?