unscrew the extender, use hemostats to fiddle around inside the rim and loosen the presta valve..
on the next tire make sure to get one with a valve having a removable core, and remove it into the extender itself..

Hello everyone, I know I'm late on this post but I had the same problem with my zipp303 tubular with Continental completion and Continental valve extender, it got clogged with Stan's no tubes. I couldn't inflate the tire with a floor pump. I even believe I blew the pump gasket on the pump by forcing it. However after reading this blog. I had some brainstorming trying to think what to use. I didn't have any thin, long Allen key. So I decided to use one of those HEAVY DUTY PAPERCLIPS. I was able to unclogged the valve and put air in the tire..now I will keep a couple of those in my toolbox....take care everyone.

+1

that's exactly what i do, long paper clips/ safety pins will do the trick, and i keep 2 in my wheel bag

As others have said, removable valve cores are a big help. Sometimes tubies that you expect to have removable cores don't. I use a drop of glue to keep them open.