During my hundreds of huge BGT installation which I made for the last years, when I wanted to change mod/component in the middle, I didn't remember a single case when it was successful. I know that the main reason are the game engine itself, mod coding and how weidu process tings but I urge you to improve uninstallation consistency. Maybe it won't be 100% perfect and some combination of the old mods will still produce an installation which can't be changed but for the new(EE) mods, it should be reasonable to expect fully working reinstallation of the components.
About data: I never write any notes which will have some useful debbug data for you like combination of the weidu.log + the component which I wanted to reinstall and the modname.debug to see what was going on. But I can give you new data. I can spend some time to give you exact cases when reinstallation fails.
The question is, will it be useful for you?