well.. there isn't anything special to do... just close T-Clock and extract the new files over your old ones.. worst thing that could theoretically happen, would be to have left over files lying around... (especially when coming from Stoic's original version.. though since that didn't support a portable mode, it's save to delete unless you've stored some files manually)
Except for the startup setup and user created relative paths, T-Clock doesn't really care about its location, so you could always delete the old folder (and copy/save/backup your T-Clock.ini in case the portable mode is used)