Not really sure what you mean...it makes no difference WHERE the wad is installed from...The user installed Wads that were meant to be used tor TBR...so IOS36 and 2 versions of IOS15. He then uninstalled them.Instead of placing the wad on the root, I put it in the wad folder and installed it, that was a bad for cIOS36, I overwrote my patched IOS36, and had problems ever since, and even DOP-Mii hasn't fixed my problems.
As for overwriting a patched IOS36 with an unpatched IOS... all you have to do is patch it again..? Its patched but your wii is not the same..what does that mean? Sorry, just kind of confused.