I'm not quite sure how you could do it in php (although I wouldn't give up hope - there may be a way!).
Keep in mind I use ASP every day, not PHP.
If you do end up manually editing files, you can open a hundred of them at once with Textpad and just do a global search and replace of
with nothing... I know, not the best solution but it should work in a pinch. Maybe someone else will come along with a better suggestion.
Like some way of denying any external access from the archived folders, I would imagine (except to your script). That should be possible I would think.