I'm about to purchase a 2002 WRX with the Vishnu stage 0 on it, I'm going to get a Cobb AP instead. My questions is that can I just get the AP and have it flashed over the ECU reflash from vishnu? Or do I have to bring it somewhere and have the ECU flashed back to stock before I can use the AP?

You should be able to flash right over it. Once you flash over it, it is GONE, so be sure you don't care about the Vishnu flash.

And before someone posts it, NO the AP does NOT save the flash you had on there before. When you unmarry it, it goes back to a factory Subaru image. That Vishnu flash is history.