Even though the site is PHP/MySQL driven, it sounds as though your VB.net application is actually doing the work. Since this is a PHP site and I am not familiar with VB.net, I can't really say for sure, but can you "reverse engineer" the mechanism you implemented to download it in the first place?
I may be mistaken in how I am interpreting your post, so I apologize if I am. Maybe give more details about what you are doing, and how you are doing it, and we can maybe help you along.