I have a mod 4.3 TW ROM that has been themed with a zip that was flashed on top of it. If I flash another theme on top of it, it messes up the phone. The only way I have found to re-theme is to dirty flash the initial ROM on top while purging the system files prior.
What happens is that the phone keeps all my data, the theme is gone, yet all the system files are back including bloat which takes a very long time to remove. Then after purging a large amount of system files I don't want that were reinstalled, then I can finally flash a new theme.
Wasn't sure if there was an easier way.