The files can be saved in TD2 or TD3 install folder. Unless I'm mistaken, you can make it point to any file in any folder, and the program will open it. TD3 on it's own will not know that you uninstalled previous versions of the software, so you should have to re-point it to where you want it to look.
Are you saying that you did this, and it still is wanting to look at the old locations? If so, that sounds to me to be a bug (but I'm not a programmer, so I can't say). If this is the case, I can say that this happened to me too, albeit I have yet to uninstall TD2 (honestly, I doubt I will even though beta is discontinued).