I updated my iPhone recently - 1.1.4 - as well as the newest iTunes update a few days prior. My ringtones have disappeared from my iTunes ringtones folder and of course from my iPhone. They are nowhere to be found. BTW, my iTunes was reset not to display the ringtones column too.
I had to fully restore my phone after update. I lost all music, ringtones, but it kept all 300+ contacts and emails, plus 3 email accounts and favorites.
I was surprised, but did see note backing up iphone while it was trying to install update.
Music was only thing lost and it is in library so very easy to add back to phone.