I can assure you that none of your shows have disappeared in the changeover. It's true that we have made a lot of changes to the navigation of the site, so let me help you find them:
Be sure you are logged in, then rollover "My Shows" in the top navigation bar, then select "All (Mix)". This will take you to a page displaying each individual show you are subscribed to. Then on the right side of the page you will see a "Playlist Browser" which displays all of your current episodes. The playlist only displays up to 25 episodes at a time, so to skip to the next bunch, click the little blue arrows near the bottom of the playlist.
Finally, rollover any episode in your "Playlist Browser" and click the Play button to begin playing from your playlist.
Hopefully this helps, and let me know if you have any more questions with our transition to the new site!