Ok....I have experienced this not once but twice. My URL rewrite rules will disappear completely after they are saved and working. I don't get it. I am using the IIS Rewrite module with remote IIS admin. I save the rules, the site works as it should and then poof....
Those rules are saved in the web.config file in your site's root directory, so if you overwrite web.config the IIS Manager changes will disappear.