How do i stop the website from updating my textures, so that i can put a file into my custom folder and have it stay there, without it being overwritten by my uploaded one.

you cant, only if you make all your custom folder Read-Only.
If you do so, you wont be able to update it, as Toribash wont be able to update it either, so you'll stick with the textures you set there.

Is it possible to change the files back?

Well you set it read only then you can reset it to normal, of course.

Ok, that helps heaps. Thanks.