I believe I have fixed the issue on the website with downloading or playing episodes. I have fixed from episode 206 on. Episodes 206+ should now download correctly, and the webplayer on the site should also work for these episodes.
Make sure you refresh/reload the page if you're trying to download from the site, so that you're not using a cached version of the page. If you're using iTunes, or an app that uses iTunes' database, it may take a few hours for iTunes to update. However, if you're using an app subscribed via the RSS feed, the updates should be live, just refresh the feed in your app.
If anyone is still having issues with episode 206-211 after this change, please let me know. Once this is confirmed to be working, I'll start the insanely time-consuming task of re-uploading the other 210 episodes. :/