the method that most posts about this problem end up referring to is the following one;
http://rtw.heavengames.com/cgi-bin/f...&f=3,3340,,all
Personally, I've never had to use this method.
One thing you may consider for the future is to keep a clean (i.e. unmodded) version of RTW 1.5 RTW 1.6. Each time you want a new mod (or once for mod folder versions) take a copy of the folder and simply apply mods to that. You should never need to go through the uninstall / install process ever again. That is unless you really do want to completely remove RTW from your machine.