After upgrading to the latest version of Webkit ALL my settings got deleted. (Bookmarks, View settings, tabs, home page, everything.) Not sure what the problem is, but it deleted it on both Safari and Webkit.
The nightly builds of WebKit just launch your installed version of Safari with the new version of the WebKit frameworks. WebKit itself does not touch Safari's preferences or data files. If there is a problem here, it would be in Safari rather than WebKit. You should re-file this bug report at <http://bugreport.apple.com/>, which is where reports of problems in Safari should be filed. Thanks!
No follow-up: INVALID.