I’ve gotten the impression that when you connect your Clip to an external computer, the storage (whatever the mode) is not always mirrored correctly, and that’s a problem that as a user you probably cannot solve. For instance, in MTP mode I had two Playlists folders with identical contents for a while, when viewed on my computer. That’s something that should never happen. I’ve also deleted files and folders on the computer and not have them go away on the Clip. Running in Auto mode probably exacerbates this problem and may account for your difficulties, @vconover.
For what it’s worth, I’m mostly working in Linux and now use MTP mode in Linux as my main way of managing my Clip+. Under Linux, mtpfs is your friend.
