I recently had to uninstall/reinstall my brew casks and recipies because I had royally screwed something up. I have a script to re-install all the things I want so it was no drama except for the downloads and re-install, and some oversights when I uninstalled brew. So here is what I think I should have done:

1. uninstall any applications installed with brew cask

$ for APP in $(brew cask list); do
  brew cask uninstall $APP
done

2. uninstall Homebrew:

(see the install/uninstall help on GitHub)

$ http https://raw.githubusercontent.com/Homebrew/install/master/uninstall  > uninstall #or curl -fsSL
$ chmod +x uninstall
$ ./uninstall --help
$ ./uninstall --force

3. re-install Homebrew

Either run the installer as described, or use my dotfiles which takes care of everything.