Music, Podcasts, and Movies disappeared from my iPhone
Although I cannot account for the loss of the media, and the used storage on the phone may or may not include the ghosts of those files, here is what I did. I first backed up iTunes and archived the iPhone backup for safety, and then I synced (as per Apple Support advice) to iTunes, and everything copied itself over to the iPhone, it appears like normal again, which is great.

The only thing was that Podcasts tried to download a bunch of podcasts that had already copied on to the iPhone from iTunes, so I canceled those downloads. Not sure why it wanted to download what it already had.

Again, I can't figure out the cause or if this is a common occurrence, but it appears okay for now.