Several years back, I made the mistake of checking the option on my iPhone to "sync subscriptions" for podcasts. I later deleted a podcast from my phone, as I was all caught up with it and needed the screen real estate to make looking for other podcasts easier. When I next synced with iTunes, it deleted all past episodes I had stored on my Mac -- years worth of the science fiction podcast Escape Pod. No warning, no recycle bin. Gone. And I wasn't backing up audio files via Time Machine because of their size. Hundreds of files gone.
I posted on the Apple forums about what a huge hole this was (seriously, deleting hundreds of user files without warning with no undo is a major UX/UI failing). Never any response from Apple.
I'm still angry about it. Even if I were to download all those files again (and since they're no longer in the iTunes feed, I would literally have to grab each one from the website, one by one, and then import them into iTunes, which would probably take days of clicking...), I would still have lost the metadata (play dates, counts). Plus there would be considerable bandwidth for both the Escape Pod site and me, in this age of looming data caps...