I just updated by subscription to the Sound of the Day podcast in iTunes and the missing shows are now available! I still don't know what went wrong, but I'll keep a closer eye on future posts to make sure they are available via iTunes.
I have gone through each of the "missing" shows from the iTunes music store, moved data around and put it back in place to see if this feed just needed someone to kick the tires and get it back online. Now all the enclosures are showing up in the Feedburner feed, so I think it might have worked.
The iTunes music store listings have not updated as of this writing, but I'm hoping it will be fixed soon.
Thanks for your patience during this period of growing pains.