Add this to Web.Config under the
Azure WebApp Quirk: Restart the WebApp
Even though I did a deployment ,manual hack of the web.config to test stuff it still refused find the Woff files. The deployment and the manual changing of the Web.Config should in traditional IIS restarted the app pool and reloaded the whole app. Even hacking the web.config so it brought down the app with 500 errors and changing it back still didn't fix it.
Only restarting the web app worked. Burned an hour on a trivial fix.