I'd love to get these kind of issues reported to me so they could be solved. I can't think situation where reflash is required since Theme Customizer only edits theme files and if something goes wrong, you can always restore from backup or reinstall the theme (yes, you can reinstall the built-in ones also by typing this into terminal:
sudo gainroot
apt-get install hildon-theme-alpha --reinstall
apt-get install hildon-theme-beta --reinstall

With latest version of Theme Customizer you can also save your theme as new theme so you'll always have the original in safe in case something goes wrong.